diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..1b1dda5f
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,6 @@
+.git
+.github
+.nextflow*
+.nextflow.log*
+work/
+results/
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml.disabled
similarity index 100%
rename from .github/workflows/awsfulltest.yml
rename to .github/workflows/awsfulltest.yml.disabled
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml.disabled
similarity index 100%
rename from .github/workflows/awstest.yml
rename to .github/workflows/awstest.yml.disabled
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml.disabled
similarity index 100%
rename from .github/workflows/branch.yml
rename to .github/workflows/branch.yml.disabled
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml.disabled
similarity index 100%
rename from .github/workflows/ci.yml
rename to .github/workflows/ci.yml.disabled
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml.disabled
similarity index 100%
rename from .github/workflows/clean-up.yml
rename to .github/workflows/clean-up.yml.disabled
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml.disabled
similarity index 100%
rename from .github/workflows/download_pipeline.yml
rename to .github/workflows/download_pipeline.yml.disabled
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml.disabled
similarity index 100%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix-linting.yml.disabled
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml.disabled
similarity index 100%
rename from .github/workflows/linting.yml
rename to .github/workflows/linting.yml.disabled
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml.disabled
similarity index 100%
rename from .github/workflows/linting_comment.yml
rename to .github/workflows/linting_comment.yml.disabled
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml.disabled
similarity index 100%
rename from .github/workflows/release-announcements.yml
rename to .github/workflows/release-announcements.yml.disabled
diff --git a/.gitignore b/.gitignore
index 441060fb..4364d586 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,5 @@ R_sessionInfo.log
.vscode/
profile.svg
+
+.latch/.logs
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-04e31f/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-04e31f/docker-build-logs.txt
new file mode 100644
index 00000000..0e3b9be1
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-04e31f/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 3130bdb47e3b
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 1a3875c24100
+
+ ---> 81ecc678fa8c
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in a1e153766787
+
+ ---> 1db50306d0e6
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in b5b897a3da23
+
+ ---> 230f37d31b1c
+
+Successfully built 230f37d31b1c
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-04e31f
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-0bd102/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-0bd102/docker-build-logs.txt
new file mode 100644
index 00000000..7677a393
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-0bd102/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> dad6ab07ea8c
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 7d31976c569c
+
+ ---> b1c55a307188
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 5fa81e1e8c1f
+
+ ---> d39c058d6be3
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 04fa31636ed1
+
+ ---> d2fd0276f2d2
+
+Successfully built d2fd0276f2d2
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-0bd102
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-14b20d/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-14b20d/docker-build-logs.txt
new file mode 100644
index 00000000..d95a8806
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-14b20d/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 2b71d40a148e
+
+Step 10/12 : arg tag
+
+
+ ---> Running in b16d629ad398
+
+ ---> ea84f03714a6
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 29ebfa3ab767
+
+ ---> 29264892e6b9
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 90cfd5010b9d
+
+ ---> 3a019d9bf388
+
+Successfully built 3a019d9bf388
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-14b20d
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-15bc6c/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-15bc6c/docker-build-logs.txt
new file mode 100644
index 00000000..b670ad79
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-15bc6c/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 9e03c04bae9d
+
+Step 10/12 : arg tag
+
+
+ ---> Running in cdd6af3b7e8e
+
+ ---> 6d7e0cacd835
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in f1a23b89a2a7
+
+ ---> 3fce6f74d6eb
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 712abffd8a6e
+
+ ---> 6003ee35c04d
+
+Successfully built 6003ee35c04d
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-15bc6c
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-1bcd35/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-1bcd35/docker-build-logs.txt
new file mode 100644
index 00000000..1f1a2f53
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-1bcd35/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 0cf27bb31ca3
+
+Step 10/12 : arg tag
+
+
+ ---> Running in e0dc8b7faa3c
+
+ ---> 0da3c7991f84
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 3ea16f201802
+
+ ---> 04f5e600c34a
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in e8fc1b0af7ee
+
+ ---> 69c8d27bff4c
+
+Successfully built 69c8d27bff4c
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-1bcd35
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-28232c/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-28232c/docker-build-logs.txt
new file mode 100644
index 00000000..503dc02d
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-28232c/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> df6c61763974
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 1655d764151f
+
+ ---> d5ac8ad639d8
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 6e67844d526c
+
+ ---> 4321d2715fe1
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 9fc7673c082e
+
+ ---> 376c3da17a89
+
+Successfully built 376c3da17a89
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-28232c
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-2d9182/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-2d9182/docker-build-logs.txt
new file mode 100644
index 00000000..3ca8bd1a
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-2d9182/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 86a3e7c47da1
+
+Step 10/12 : arg tag
+
+
+ ---> Running in ae1ba8af9dc1
+
+ ---> ad7fc24753e2
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 9aa1737e3715
+
+ ---> 6a435cb9668d
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in aeec25ed1a37
+
+ ---> d1781653c28c
+
+Successfully built d1781653c28c
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-2d9182
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-351d10/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-351d10/docker-build-logs.txt
new file mode 100644
index 00000000..7b3ca337
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-351d10/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 9e902eae1ea3
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 9d14e5bfa7e3
+
+ ---> a9603d3d47d5
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 59d4e38914de
+
+ ---> 85ac530a6088
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 6329d55db208
+
+ ---> 0625de06e6b6
+
+Successfully built 0625de06e6b6
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-351d10
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-4c5052/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-4c5052/docker-build-logs.txt
new file mode 100644
index 00000000..9daa074b
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-4c5052/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> d56a4a17371a
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 59b51360e9d2
+
+ ---> 40baa7e11f61
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in ccefa83d7447
+
+ ---> 406577834233
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 0d74d18aa13c
+
+ ---> 5135d419a599
+
+Successfully built 5135d419a599
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-4c5052
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-56df58/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-56df58/docker-build-logs.txt
new file mode 100644
index 00000000..48961901
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-56df58/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> fd5ff9c9acca
+
+Step 10/12 : arg tag
+
+
+ ---> Running in f3e620f8173b
+
+ ---> 0bf3e95c8497
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 7c27dc3d39d0
+
+ ---> a8fafea98738
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in da1ce8022b3f
+
+ ---> 20c8e1b175ba
+
+Successfully built 20c8e1b175ba
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-56df58
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-57ae63/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-57ae63/docker-build-logs.txt
new file mode 100644
index 00000000..5eaeb541
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-57ae63/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 6498c04066c2
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 85506ce9ccb0
+
+ ---> f30f694fad09
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 77f9c7f10e3b
+
+ ---> 82ad3122a40a
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in da469e851fae
+
+ ---> 059f9d5e2015
+
+Successfully built 059f9d5e2015
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-57ae63
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-71d084/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-71d084/docker-build-logs.txt
new file mode 100644
index 00000000..0c105787
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-71d084/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> ab50ac925e84
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 08c9a5181214
+
+ ---> a9ce6e06c1b2
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in f4f18366d429
+
+ ---> c86d559b66ae
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in c74ea9314522
+
+ ---> aecc8ad07262
+
+Successfully built aecc8ad07262
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-71d084
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-763f25/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-763f25/docker-build-logs.txt
new file mode 100644
index 00000000..253473e6
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-763f25/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 948f188bc47e
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 0d435207e1e4
+
+ ---> cf42fa807751
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in dd3d64721195
+
+ ---> e4d30c90f749
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 44fff340fede
+
+ ---> 0750b4e836ee
+
+Successfully built 0750b4e836ee
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-763f25
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-865dcb/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-865dcb/docker-build-logs.txt
new file mode 100644
index 00000000..409966ae
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-865dcb/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v1.1.7
+
+
+ ---> 884f8e5666b5
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 6b89f6228cb4
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> 080efe1dfb73
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> e7bc60ad5baf
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> e133f72562f7
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 85d9823692d7
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> 502514529836
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 4fdeaac6d35e
+
+Step 9/12 : copy . /root/
+
+
+ ---> 7fb99a22e6d8
+
+Step 10/12 : arg tag
+
+
+ ---> Running in b0733796081d
+
+ ---> 0d641350b361
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 61875c7c145d
+
+ ---> ebbfcb4bb9f9
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in c7f8d81359f8
+
+ ---> 7c557785afa8
+
+Successfully built 7c557785afa8
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-865dcb
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9567ca/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9567ca/docker-build-logs.txt
new file mode 100644
index 00000000..86cf366c
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9567ca/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 83c2c1234d8f
+
+Step 10/12 : arg tag
+
+
+ ---> Running in ebd760eba94a
+
+ ---> de28a96e6bfa
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 355dc2a6602f
+
+ ---> 32824d2075be
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 3910a6e5640a
+
+ ---> 234417e917aa
+
+Successfully built 234417e917aa
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9567ca
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-96dd33/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-96dd33/docker-build-logs.txt
new file mode 100644
index 00000000..73a48bd5
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-96dd33/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> a54c7a5429ce
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 1611dd9279c6
+
+ ---> 47275525bde6
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 6c382ae94c87
+
+ ---> b0392c15561b
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 30c93e051f0e
+
+ ---> d4c27b80d980
+
+Successfully built d4c27b80d980
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-96dd33
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-987a0c/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-987a0c/docker-build-logs.txt
new file mode 100644
index 00000000..8457eb41
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-987a0c/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 80c0c7de0ca1
+
+Step 10/12 : arg tag
+
+
+ ---> Running in d4a11d3c466c
+
+ ---> 307c0bfb46f1
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in cdea3d937214
+
+ ---> c06512a702a1
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 82d651df758b
+
+ ---> e79a074ad077
+
+Successfully built e79a074ad077
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-987a0c
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9e0fe1/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9e0fe1/docker-build-logs.txt
new file mode 100644
index 00000000..1f500d2d
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9e0fe1/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> da49a31cd89a
+
+Step 10/12 : arg tag
+
+
+ ---> Running in abb202537cc8
+
+ ---> ea17cc31efec
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in e9fbc06d136d
+
+ ---> 8c0281c60154
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in bab07333531b
+
+ ---> 284ec5d8892f
+
+Successfully built 284ec5d8892f
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-9e0fe1
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ad261b/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ad261b/docker-build-logs.txt
new file mode 100644
index 00000000..e1550004
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ad261b/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v1.1.7
+
+
+ ---> 884f8e5666b5
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 6b89f6228cb4
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> 080efe1dfb73
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> e7bc60ad5baf
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> e133f72562f7
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 85d9823692d7
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> 502514529836
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 4fdeaac6d35e
+
+Step 9/12 : copy . /root/
+
+
+ ---> 68e7c42af2d2
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 5de5a6584537
+
+ ---> 839ef0abb1ed
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in dc7144ebbcae
+
+ ---> f98bfd798675
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 880b42e59ec1
+
+ ---> 44927ce39de0
+
+Successfully built 44927ce39de0
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ad261b
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b518a6/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b518a6/docker-build-logs.txt
new file mode 100644
index 00000000..854aebe6
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b518a6/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> ed8ee87027ef
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 40213fe84693
+
+ ---> 9148e50c4420
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in e7368bf4feda
+
+ ---> 2edcdd39e86a
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 88d0bd161d4b
+
+ ---> aee832deebf2
+
+Successfully built aee832deebf2
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b518a6
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b7129c/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b7129c/docker-build-logs.txt
new file mode 100644
index 00000000..cd306bc1
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b7129c/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 5202980fdfb1
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 1c5b68e98fbe
+
+ ---> 844b80cb292d
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 0901e39d7535
+
+ ---> 5f8bcc67ec30
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 72f7b313cdf3
+
+ ---> 95e59381e04f
+
+Successfully built 95e59381e04f
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-b7129c
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-bf27db/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-bf27db/docker-build-logs.txt
new file mode 100644
index 00000000..ae48e390
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-bf27db/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> fb87264e5e17
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 2f8f5e5a25e6
+
+ ---> 6f0e0e7ac98c
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 3a3b32bd4042
+
+ ---> 71bd7b5475b0
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 668b5d8572a1
+
+ ---> bf9ee4dbd608
+
+Successfully built bf9ee4dbd608
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-bf27db
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-c42ac6/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-c42ac6/docker-build-logs.txt
new file mode 100644
index 00000000..11f1a9ad
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-c42ac6/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 6b2a58419862
+
+Step 10/12 : arg tag
+
+
+ ---> Running in f08de6a53165
+
+ ---> d9b4b6ed986b
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 7384af432323
+
+ ---> 6c221db07603
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in d41636d08961
+
+ ---> 65bf49e78c98
+
+Successfully built 65bf49e78c98
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-c42ac6
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-cba6dd/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-cba6dd/docker-build-logs.txt
new file mode 100644
index 00000000..ed1de1be
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-cba6dd/docker-build-logs.txt
@@ -0,0 +1,80 @@
+Step 1/15 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base:fe0b-main
+
+
+ ---> f23c37efcd53
+
+Step 2/15 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> dd16c2d4f334
+
+Step 3/15 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> aaada0c60239
+
+Step 4/15 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> d6869bc03deb
+
+Step 5/15 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> ae2f7ca65880
+
+Step 6/15 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> f029b3f36a86
+
+Step 7/15 : run pip install latch==2.46.6
+
+
+ ---> Using cache
+
+ ---> be1350f11537
+
+Step 8/15 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> e8dd4419614b
+
+Step 9/15 : run apt-get update && apt-get install -y default-jre-headless
+
+
+ ---> Using cache
+
+ ---> 447cbd90cbc9
+
+Step 10/15 : copy . /root/
+
+
+ ---> 58b86d8aeb3f
+
+Step 11/15 : run ln -s /root/.latch/bin/nextflow /root/nextflow
+
+
+ ---> Running in 8d5137feef53
+
+[91mln -s /root/.latch/bin/nextflow /root/nextflow
+[0m
+ ---> 13a37c04603e
+
+Step 12/15 : run ln -s /root/.latch/.nextflow /root/.nextflow
+
+
+ ---> Running in 4bae33b8f040
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d14dd7/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d14dd7/docker-build-logs.txt
new file mode 100644
index 00000000..5364ad69
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d14dd7/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v1.1.7
+
+
+ ---> 884f8e5666b5
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 6b89f6228cb4
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> 080efe1dfb73
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> e7bc60ad5baf
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> e133f72562f7
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 85d9823692d7
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> 502514529836
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 4fdeaac6d35e
+
+Step 9/12 : copy . /root/
+
+
+ ---> 25923086db67
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 0cdf7eb3a530
+
+ ---> 5fcdc30e5af1
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 84e637cb6492
+
+ ---> 19d31264f1c9
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in f2eb7b9dd166
+
+ ---> 5775a2145175
+
+Successfully built 5775a2145175
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d14dd7
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-db89d4/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-db89d4/docker-build-logs.txt
new file mode 100644
index 00000000..0c2fd0bf
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-db89d4/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> eb2c2fb37151
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 25bd95ce489d
+
+ ---> f100e8ae53c5
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 9bc6163eed9c
+
+ ---> 8fb41777054e
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 1d59e237aaea
+
+ ---> c0f4d089b410
+
+Successfully built c0f4d089b410
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-db89d4
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ddb034/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ddb034/docker-build-logs.txt
new file mode 100644
index 00000000..57c6239c
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ddb034/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 23f11d8c7f4f
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 41abaeb60b2f
+
+ ---> 7e2cba0ae234
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in f4a0f5372c9a
+
+ ---> 2fed004bf78f
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 70f2d67cfc80
+
+ ---> 972d51653358
+
+Successfully built 972d51653358
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ddb034
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e3cb14/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e3cb14/docker-build-logs.txt
new file mode 100644
index 00000000..d5435c2c
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e3cb14/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 1c732fdf2616
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 68d1d8ce3735
+
+ ---> 7b4d0911ff76
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 675698d063d5
+
+ ---> 1a18d54baf74
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 2ed19cf8d53f
+
+ ---> 72d333f861ca
+
+Successfully built 72d333f861ca
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e3cb14
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e9d826/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e9d826/docker-build-logs.txt
new file mode 100644
index 00000000..e0d1a63c
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e9d826/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> ed363dd4c45a
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 8224340eed49
+
+ ---> 7615be778d2e
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in b5ab54c2895a
+
+ ---> 95a3e1a00804
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 38b6e8c1bd26
+
+ ---> 46519672244d
+
+Successfully built 46519672244d
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-e9d826
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ebd0e4/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ebd0e4/docker-build-logs.txt
new file mode 100644
index 00000000..75484f51
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ebd0e4/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 667dcc48b428
+
+Step 10/12 : arg tag
+
+
+ ---> Running in b3354a35275a
+
+ ---> bad87e668109
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in db82dda85426
+
+ ---> fbcc83f767f9
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in e59e8f4d4a98
+
+ ---> fd061e695587
+
+Successfully built fd061e695587
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ebd0e4
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ecbaf0/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ecbaf0/docker-build-logs.txt
new file mode 100644
index 00000000..704a8b1c
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ecbaf0/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 9dcf2cb19fde
+
+Step 10/12 : arg tag
+
+
+ ---> Running in e66916bdeda8
+
+ ---> 05e249ff80fa
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 083c1bb91e55
+
+ ---> f187b7a7cc14
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 5c432580db84
+
+ ---> dbb5da47cf1c
+
+Successfully built dbb5da47cf1c
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-ecbaf0
+
diff --git a/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-f07047/docker-build-logs.txt b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-f07047/docker-build-logs.txt
new file mode 100644
index 00000000..83923260
--- /dev/null
+++ b/.latch/.logs/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-f07047/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 3964add1db13
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 536cd810a243
+
+ ---> 4027320badd1
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in cf5b952816ef
+
+ ---> ae6a0e53da54
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 07e5b74335fc
+
+ ---> c9f4f04759c3
+
+Successfully built c9f4f04759c3
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35729_nf_nf_core_cutandrun:0.1.0-96a42f-wip-f07047
+
diff --git a/.latch/.logs/35929_nf_nf_core_cutandrun:0.1.0-96a42f-wip-da774b/docker-build-logs.txt b/.latch/.logs/35929_nf_nf_core_cutandrun:0.1.0-96a42f-wip-da774b/docker-build-logs.txt
new file mode 100644
index 00000000..3bfdbcda
--- /dev/null
+++ b/.latch/.logs/35929_nf_nf_core_cutandrun:0.1.0-96a42f-wip-da774b/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> a73027c4df84
+
+Step 10/12 : arg tag
+
+
+ ---> Running in 3d21c680e2d8
+
+ ---> 77ee5fed91c2
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in 881bcf04697e
+
+ ---> b31226e90f38
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 24e7738bf159
+
+ ---> e222219fed2d
+
+Successfully built e222219fed2d
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/35929_nf_nf_core_cutandrun:0.1.0-96a42f-wip-da774b
+
diff --git a/.latch/.logs/36340_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d6e2a4/docker-build-logs.txt b/.latch/.logs/36340_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d6e2a4/docker-build-logs.txt
new file mode 100644
index 00000000..95520f1d
--- /dev/null
+++ b/.latch/.logs/36340_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d6e2a4/docker-build-logs.txt
@@ -0,0 +1,84 @@
+Step 1/12 : from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.0.0
+
+
+ ---> 98d9cd0f2a3a
+
+Step 2/12 : workdir /tmp/docker-build/work/
+
+
+ ---> Using cache
+
+ ---> 8f95defb9629
+
+Step 3/12 : shell [ "/usr/bin/env", "bash", "-o", "errexit", "-o", "pipefail", "-o", "nounset", "-o", "verbose", "-o", "errtrace", "-O", "inherit_errexit", "-O", "shift_verbose", "-c" ]
+
+
+ ---> Using cache
+
+ ---> b2b2f8c4e3df
+
+Step 4/12 : env TZ='Etc/UTC'
+
+
+ ---> Using cache
+
+ ---> ee07cb31686a
+
+Step 5/12 : env LANG='en_US.UTF-8'
+
+
+ ---> Using cache
+
+ ---> b133cffabb9a
+
+Step 6/12 : arg DEBIAN_FRONTEND=noninteractive
+
+
+ ---> Using cache
+
+ ---> 7f1ec8bb956e
+
+Step 7/12 : run pip install latch==2.52.1
+
+
+ ---> Using cache
+
+ ---> f6fd6659b394
+
+Step 8/12 : run mkdir /opt/latch
+
+
+ ---> Using cache
+
+ ---> 48d9448c23ba
+
+Step 9/12 : copy . /root/
+
+
+ ---> 16fcabb41c1c
+
+Step 10/12 : arg tag
+
+
+ ---> Running in a303f7429f36
+
+ ---> 049d0a9255e6
+
+Step 11/12 : env FLYTE_INTERNAL_IMAGE $tag
+
+
+ ---> Running in ecd02faaa3de
+
+ ---> d489b7c09ede
+
+Step 12/12 : workdir /root
+
+
+ ---> Running in 5565daeeb7cc
+
+ ---> 40bda76ee715
+
+Successfully built 40bda76ee715
+
+Successfully tagged 812206152185.dkr.ecr.us-west-2.amazonaws.com/36340_nf_nf_core_cutandrun:0.1.0-96a42f-wip-d6e2a4
+
diff --git a/.latch/Dockerfile b/.latch/Dockerfile
new file mode 100644
index 00000000..49f6c543
--- /dev/null
+++ b/.latch/Dockerfile
@@ -0,0 +1,39 @@
+# DO NOT CHANGE
+from 812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.1.2
+
+workdir /tmp/docker-build/work/
+
+shell [ \
+ "/usr/bin/env", "bash", \
+ "-o", "errexit", \
+ "-o", "pipefail", \
+ "-o", "nounset", \
+ "-o", "verbose", \
+ "-o", "errtrace", \
+ "-O", "inherit_errexit", \
+ "-O", "shift_verbose", \
+ "-c" \
+]
+env TZ='Etc/UTC'
+env LANG='en_US.UTF-8'
+
+arg DEBIAN_FRONTEND=noninteractive
+
+# Latch SDK
+# DO NOT REMOVE
+run pip install latch==2.52.1
+run mkdir /opt/latch
+
+
+# Copy workflow data (use .dockerignore to skip files)
+
+copy . /root/
+
+
+# Latch workflow registration metadata
+# DO NOT CHANGE
+arg tag
+# DO NOT CHANGE
+env FLYTE_INTERNAL_IMAGE $tag
+
+workdir /root
diff --git a/.latch/config b/.latch/config
new file mode 100644
index 00000000..14a68ec5
--- /dev/null
+++ b/.latch/config
@@ -0,0 +1 @@
+{"latch_version": "2.52.1", "base_image": "812206152185.dkr.ecr.us-west-2.amazonaws.com/latch-base-nextflow:v2.1.2", "date": "2024-09-12T12:57:15.404807"}
diff --git a/.latch/workflow_name b/.latch/workflow_name
new file mode 100644
index 00000000..5a6730b4
--- /dev/null
+++ b/.latch/workflow_name
@@ -0,0 +1 @@
+nf_nf_core_cutandrun
\ No newline at end of file
diff --git a/latch.config b/latch.config
new file mode 100644
index 00000000..b8e37106
--- /dev/null
+++ b/latch.config
@@ -0,0 +1,9 @@
+process {
+ executor = 'k8s'
+}
+
+aws {
+ client {
+ anonymous = true
+ }
+}
diff --git a/latch_metadata/__init__.py b/latch_metadata/__init__.py
new file mode 100644
index 00000000..bad6f293
--- /dev/null
+++ b/latch_metadata/__init__.py
@@ -0,0 +1,187 @@
+from latch.types.directory import LatchDir
+from latch.types.metadata import (
+ Fork,
+ ForkBranch,
+ LatchAuthor,
+ NextflowMetadata,
+ NextflowRuntimeResources,
+ Params,
+ Section,
+ Spoiler,
+ Text,
+)
+
+from .parameters import generated_parameters
+
+flow = [
+ Section(
+ "Input",
+ Params("input"),
+ Text("Samplesheet expects 'control' column to be filled for all non-control samples."),
+ Spoiler(
+ "Optional",
+ Params("use_control"),
+ ),
+ ),
+ Section(
+ "Reference Genome Options",
+ Fork(
+ "genome_source",
+ "",
+ latch_genome_source=ForkBranch("Latch Certified Reference Genome", Params("latch_genome")),
+ input_ref=ForkBranch(
+ "Custom Reference Genome",
+ Params("fasta", "gtf"),
+ Spoiler(
+ "Reference Options",
+ Params("gene_bed", "save_reference"),
+ Text(
+ "The transcriptome and GTF files in iGenomes are vastly out of date with respect to current annotations from Ensembl e.g. human iGenomes annotations are from Ensembl release 75, while the current Ensembl release is 108. Please consider downloading and using a more updated version of your reference genome."
+ ),
+ Params("genome"),
+ ),
+ ),
+ ),
+ ),
+ Spoiler(
+ "Spikein Genome Options",
+ Params(
+ "spikein_genome",
+ "spikein_bowtie2",
+ "spikein_fasta",
+ "save_spikein_aligned",
+ ),
+ ),
+ Section(
+ "Output Directory",
+ Params("run_name"),
+ Text("Parent directory for outputs"),
+ Params("outdir"),
+ ),
+ Spoiler(
+ "Optional Parameters",
+ Spoiler(
+ "Alignment Filters",
+ Params(
+ "bowtie2",
+ "blacklist",
+ "remove_mitochondrial_reads",
+ "mito_name",
+ "minimum_alignment_q_score",
+ "save_unaligned",
+ "save_align_intermed",
+ "remove_linear_duplicates",
+ "end_to_end",
+ ),
+ ),
+ Spoiler(
+ "Peak Calling Options",
+ Params("peakcaller"),
+ Spoiler(
+ "MACS2 Optional Parameters",
+ Params(
+ "macs2_qvalue",
+ "macs2_pvalue",
+ "macs_gsize",
+ "macs2_narrow_peak",
+ "macs2_broad_cutoff",
+ "consensus_peak_mode",
+ "replicate_threshold",
+ "extend_fragments",
+ ),
+ ),
+ Spoiler(
+ "SEACR Options",
+ Params(
+ "seacr_peak_threshold",
+ "seacr_norm",
+ "seacr_stringent",
+ ),
+ ),
+ ),
+ Spoiler(
+ "Read trimming and QC Options",
+ Params(
+ "save_merged_fastq",
+ "save_trimmed",
+ "clip_r1",
+ "clip_r2",
+ "three_prime_clip_r1",
+ "three_prime_clip_r2",
+ "trim_nextseq",
+ "dedup_target_reads",
+ ),
+ ),
+ Spoiler(
+ "Normalization Options",
+ Params("normalisation_mode", "normalisation_binsize", "igg_scale_factor", "dump_scale_factors"),
+ ),
+ Spoiler(
+ "Reporting/Plotting Options",
+ Params(
+ "dt_qc_bam_binsize",
+ "dt_qc_corr_method",
+ "dt_calc_all_matrix",
+ "dt_heatmap_gene_beforelen",
+ "dt_heatmap_gene_bodylen",
+ "dt_heatmap_gene_afterlen",
+ "dt_heatmap_peak_beforelen",
+ "dt_heatmap_peak_afterlen",
+ "min_frip_overlap",
+ "min_peak_overlap",
+ "igv_show_gene_names",
+ "igv_sort_by_groups",
+ ),
+ ),
+ Spoiler(
+ "Flow Switching Options",
+ Params(
+ "only_input",
+ "only_genome",
+ "only_preqc",
+ "only_alignment",
+ "only_filtering",
+ "only_peak_calling",
+ ),
+ ),
+ Spoiler(
+ "Skip Tools",
+ Params(
+ "skip_fastqc",
+ "skip_trimming",
+ "skip_removeduplicates",
+ "skip_reporting",
+ "skip_preseq",
+ "skip_igv",
+ "skip_dt_qc",
+ "skip_heatmaps",
+ "skip_peak_qc",
+ "skip_multiqc",
+ ),
+ ),
+ Spoiler(
+ "MultiQC Options",
+ Params(
+ "multiqc_title",
+ "multiqc_methods_description",
+ ),
+ ),
+ ),
+]
+
+
+NextflowMetadata(
+ display_name="nf-core/cutandrun",
+ author=LatchAuthor(
+ name="nf-core",
+ ),
+ repository="https://github.com/latchbio-nfcore/cutandrun",
+ parameters=generated_parameters,
+ runtime_resources=NextflowRuntimeResources(
+ cpus=4,
+ memory=8,
+ storage_gib=100,
+ ),
+ log_dir=LatchDir("latch:///your_log_dir"),
+ flow=flow,
+)
diff --git a/latch_metadata/parameters.py b/latch_metadata/parameters.py
new file mode 100644
index 00000000..63b18f04
--- /dev/null
+++ b/latch_metadata/parameters.py
@@ -0,0 +1,593 @@
+from dataclasses import dataclass
+from enum import Enum
+from typing import List, Optional
+
+from latch.types.directory import LatchDir, LatchOutputDir
+from latch.types.file import LatchFile
+from latch.types.metadata import LatchRule, Multiselect, NextflowParameter
+
+
+@dataclass
+class SampleSheet:
+ group: str
+ replicate: int
+ fastq_1: LatchFile
+ fastq_2: LatchFile
+ control: Optional[str]
+
+
+class Reference(Enum):
+ hg38 = "GRCh38 (Homo Sapiens hg38)"
+ hg19 = "GRCh37 (Homo Sapiens hg19)"
+
+
+generated_parameters = {
+ "input": NextflowParameter(
+ type=List[SampleSheet],
+ display_name="Input",
+ description="Information about the samples in the experiment",
+ section_title=None,
+ samplesheet_type="csv",
+ samplesheet=True,
+ default=None,
+ ),
+ "outdir": NextflowParameter(
+ type=LatchOutputDir,
+ default=None,
+ display_name="Outdir",
+ description="The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.",
+ ),
+ "multiqc_title": NextflowParameter(
+ type=Optional[str],
+ default=None,
+ section_title=None,
+ display_name="MultiQC Title",
+ description="MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+ ),
+ "save_reference": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Reference",
+ description="Save genome reference data to the output directory",
+ ),
+ "save_merged_fastq": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Merged FastQ",
+ description="Save any technical replicate FASTQ files that were merged to the output directory",
+ ),
+ "genome_source": NextflowParameter(
+ type=str,
+ display_name="Reference Genome",
+ description="Choose Reference Genome",
+ ),
+ "latch_genome": NextflowParameter(
+ type=Optional[Reference],
+ default=None,
+ display_name="Genome",
+ description="Name of the Latch Verfied Reference Genome",
+ ),
+ "save_trimmed": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Trimmed",
+ description="Save trimmed FASTQ files to the output directory",
+ ),
+ "save_spikein_aligned": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Spikein Aligned",
+ description="Save BAM files aligned to the spike-in genome to the output directory",
+ ),
+ "save_unaligned": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Unaligned",
+ description="Save unaligned sequences to the output directory",
+ ),
+ "save_align_intermed": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Save Align Intermed",
+ description="Save alignment intermediates to the output directory (WARNING: can be very large)",
+ ),
+ "email": NextflowParameter(
+ type=Optional[str],
+ default=None,
+ section_title=None,
+ display_name="Email",
+ description="Email address for completion summary.",
+ ),
+ "dump_scale_factors": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Dump Scale Factors",
+ description="Output calculated scale factors from pipeline",
+ ),
+ "genome": NextflowParameter(
+ type=Optional[str],
+ default=None,
+ section_title=None,
+ display_name="Genome",
+ description="Name of iGenomes reference.",
+ ),
+ "bowtie2": NextflowParameter(
+ type=Optional[LatchDir],
+ default=None,
+ section_title=None,
+ display_name="Bowtie2",
+ description="Path to bowtie2 index",
+ ),
+ "gtf": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="GTF",
+ description="Path to GTF annotation file",
+ ),
+ "gene_bed": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="Gene Bed",
+ description="Path to gene BED file",
+ ),
+ "blacklist": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="Blacklist",
+ description="Path to genome blacklist",
+ ),
+ "spikein_genome": NextflowParameter(
+ type=Optional[str],
+ default="K12-MG1655",
+ section_title=None,
+ display_name="Spikein Genome",
+ description="Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6",
+ ),
+ "spikein_bowtie2": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="Spikein Bowtie2",
+ description="Path to spike-in bowtie2 index",
+ ),
+ "spikein_fasta": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="Spikein Fasta",
+ description="Path to spike-in fasta",
+ ),
+ "fasta": NextflowParameter(
+ type=Optional[LatchFile],
+ default=None,
+ section_title=None,
+ display_name="Fasta",
+ description="Path to FASTA genome file.",
+ ),
+ "only_input": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only Input",
+ description="Run pipeline up to input checking",
+ ),
+ "only_genome": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only Genome",
+ description="Run pipeline up to reference preparation",
+ ),
+ "only_preqc": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only PreQC",
+ description="Run pipeline up to pre-alignment",
+ ),
+ "only_alignment": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only Alignment",
+ description="Run pipeline up to alignment",
+ ),
+ "only_filtering": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only Filtering",
+ description="Run pipeline up to q-filtering",
+ ),
+ "only_peak_calling": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Only Peak Calling",
+ description="Run pipeline up to peak calling",
+ ),
+ "skip_fastqc": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip FastQC",
+ description="Skips fastqc reporting",
+ ),
+ "skip_trimming": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Trimming",
+ description="Skips trimming",
+ ),
+ "skip_removeduplicates": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Remove Duplicates",
+ description="Skips de-duplication",
+ ),
+ "skip_reporting": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Reporting",
+ description="Skips reporting",
+ ),
+ "skip_preseq": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Preseq",
+ description="Skips preseq reporting",
+ ),
+ "skip_igv": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip IGV",
+ description="Skips igv session generation",
+ ),
+ "skip_dt_qc": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip DT QC",
+ description="Skips deeptools QC reporting",
+ ),
+ "skip_heatmaps": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Heatmaps",
+ description="Skips deeptools heatmap generation",
+ ),
+ "skip_peak_qc": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip Peak QC",
+ description="Skips peak QC reporting",
+ ),
+ "skip_multiqc": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Skip MultiQC",
+ description="Skips multiqc",
+ ),
+ "clip_r1": NextflowParameter(
+ type=Optional[int],
+ default=0,
+ section_title=None,
+ display_name="Clip R1",
+ description="Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).",
+ ),
+ "clip_r2": NextflowParameter(
+ type=Optional[int],
+ default=0,
+ section_title=None,
+ display_name="Clip R2",
+ description="Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).",
+ ),
+ "three_prime_clip_r1": NextflowParameter(
+ type=Optional[int],
+ default=0,
+ section_title=None,
+ display_name="Three Prime Clip R1",
+ description="Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.",
+ ),
+ "three_prime_clip_r2": NextflowParameter(
+ type=Optional[int],
+ default=0,
+ section_title=None,
+ display_name="Three Prime Clip R2",
+ description="Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.",
+ ),
+ "trim_nextseq": NextflowParameter(
+ type=Optional[int],
+ default=0,
+ section_title=None,
+ display_name="Trim NextSeq",
+ description="Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.",
+ ),
+ "minimum_alignment_q_score": NextflowParameter(
+ type=Optional[int],
+ default=20,
+ section_title=None,
+ display_name="Minimum Alignment Q Score",
+ description="Filter reads below a q-score threshold",
+ ),
+ "remove_mitochondrial_reads": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Remove Mitochondrial Reads",
+ description="Filter mitochondrial reads",
+ ),
+ "run_name": NextflowParameter(
+ type=str,
+ display_name="Run Name",
+ description="Name of run",
+ batch_table_column=True,
+ rules=[
+ LatchRule(
+ regex=r"^[a-zA-Z0-9_-]+$",
+ message="Run name must contain only letters, digits, underscores, and dashes. No spaces are allowed.",
+ )
+ ],
+ ),
+ "mito_name": NextflowParameter(
+ type=Optional[str],
+ default=None,
+ section_title=None,
+ display_name="Mito Name",
+ description="Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.",
+ ),
+ "dedup_target_reads": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Dedup Target Reads",
+ description="De-duplicate target reads AND control reads (default is control only)",
+ ),
+ "remove_linear_duplicates": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Remove Linear Duplicates",
+ description="De-duplicate reads based on read 1 5' start position. Relevant for assays using linear amplification with tagmentation (default is false).",
+ ),
+ "end_to_end": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="End to End",
+ description="Use --end-to-end mode of Bowtie2 during alignment",
+ ),
+ "normalisation_mode": NextflowParameter(
+ type=Optional[str],
+ default="Spikein",
+ section_title=None,
+ display_name="Normalisation Mode",
+ appearance_type=Multiselect(["Spikein", "RPKM", "CPM", "BPM", "None"], allow_custom=False),
+ description='Sets the target read normalisation mode. Options are: ["Spikein", "RPKM", "CPM", "BPM", "None" ]',
+ ),
+ "normalisation_binsize": NextflowParameter(
+ type=Optional[int],
+ default=50,
+ section_title=None,
+ display_name="Normalisation Binsize",
+ description='If normalisation option is one of "RPKM", "CPM", "BPM" - then the binsize that the reads count is calculated on is used.',
+ ),
+ "peakcaller": NextflowParameter(
+ type=Optional[str],
+ default="seacr",
+ section_title=None,
+ display_name="Peakcaller",
+ appearance_type=Multiselect(["seacr", "macs2"], allow_custom=False),
+ description="Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder.",
+ ),
+ "use_control": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="Use Control",
+ description="Specifies whether to use a control to normalise peak calls against (e.g. IgG)",
+ ),
+ "extend_fragments": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="Extend Fragments",
+ description="Specifies whether to extend paired-end fragments between the read mates when calculating coverage tracks",
+ ),
+ "igg_scale_factor": NextflowParameter(
+ type=Optional[float],
+ default=0.5,
+ section_title=None,
+ display_name="IGG Scale Factor",
+ description="Specifies whether the background control is scaled prior to being used to normalise peaks.",
+ ),
+ "seacr_peak_threshold": NextflowParameter(
+ type=Optional[float],
+ default=0.05,
+ section_title=None,
+ display_name="SEACR Peak Threshold",
+ description="SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if `--use_control` is `false`",
+ ),
+ "seacr_norm": NextflowParameter(
+ type=Optional[str],
+ default="non",
+ section_title=None,
+ appearance_type=Multiselect(["non", "norm"], allow_custom=False),
+ display_name="SEACR Norm",
+ description="SEACR normalization.",
+ ),
+ "seacr_stringent": NextflowParameter(
+ type=Optional[str],
+ default="stringent",
+ section_title=None,
+ appearance_type=Multiselect(["stringent", "relaxed"], allow_custom=False),
+ display_name="SEACR Stringency",
+ description="SEACR stringency.",
+ ),
+ "macs2_qvalue": NextflowParameter(
+ type=Optional[float],
+ default=0.01,
+ section_title=None,
+ display_name="MACS2 Q-value",
+ description="Q-value threshold for MACS2 peak caller.",
+ ),
+ "macs2_pvalue": NextflowParameter(
+ type=Optional[float],
+ default=None,
+ section_title=None,
+ display_name="MACS2 P-value",
+ description="P-value threshold for macs2 peak caller. If set it will override the q-value.",
+ ),
+ "macs_gsize": NextflowParameter(
+ type=Optional[float],
+ default=2700000000.0,
+ section_title=None,
+ display_name="MACS Gsize",
+ description="Parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize will default to GRCh38.",
+ ),
+ "macs2_narrow_peak": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="MACS2 Narrow Peak",
+ description="Determines whether MACS2 broad or narrow peak mode is used for the peak caller",
+ ),
+ "macs2_broad_cutoff": NextflowParameter(
+ type=Optional[float],
+ default=0.1,
+ section_title=None,
+ display_name="MACS2 Broad Cutoff",
+ description="MACS2 broad cutoff parameter",
+ ),
+ "consensus_peak_mode": NextflowParameter(
+ type=Optional[str],
+ default="group",
+ section_title=None,
+ display_name="Consensus Peak Mode",
+ appearance_type=Multiselect(["group", "all"], allow_custom=False),
+ description="Specifies what samples to group together for consensus peaks. Options are [group, all]",
+ ),
+ "replicate_threshold": NextflowParameter(
+ type=Optional[float],
+ default=1.0,
+ section_title=None,
+ display_name="Replicate Threshold",
+ description="Minimum number of overlapping replicates needed for a consensus peak",
+ ),
+ "igv_show_gene_names": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="IGV Show Gene Names",
+ description="Show gene names instead of symbols in IGV browser sessions",
+ ),
+ "dt_qc_bam_binsize": NextflowParameter(
+ type=Optional[int],
+ default=500,
+ section_title=None,
+ display_name="DT QC BAM Binsize",
+ description="Deeptools multiBamSummary bam bin size",
+ ),
+ "dt_qc_corr_method": NextflowParameter(
+ type=Optional[str],
+ default="pearson",
+ section_title=None,
+ display_name="DT QC Corr Method",
+ description="Deeptools Correlation Plot statistical calculation method",
+ ),
+ "dt_heatmap_gene_beforelen": NextflowParameter(
+ type=Optional[int],
+ default=3000,
+ section_title=None,
+ display_name="DT Heatmap Gene Beforelen",
+ description="Deeptools heatmap gene plot before length (bases)",
+ ),
+ "dt_heatmap_gene_bodylen": NextflowParameter(
+ type=Optional[int],
+ default=5000,
+ section_title=None,
+ display_name="DT Heatmap Gene Bodylen",
+ description="Deeptools heatmap gene plot body length (bases)",
+ ),
+ "dt_heatmap_gene_afterlen": NextflowParameter(
+ type=Optional[int],
+ default=3000,
+ section_title=None,
+ display_name="DT Heatmap Gene Afterlen",
+ description="Deeptools heatmap gene plot after length (bases)",
+ ),
+ "dt_heatmap_peak_beforelen": NextflowParameter(
+ type=Optional[int],
+ default=3000,
+ section_title=None,
+ display_name="DT Heatmap Peak Beforelen",
+ description="Deeptools heatmap peak plot before length (bases)",
+ ),
+ "dt_heatmap_peak_afterlen": NextflowParameter(
+ type=Optional[int],
+ default=3000,
+ section_title=None,
+ display_name="DT Heatmap Peak Afterlen",
+ description="Deeptools heatmap peak plot after length (bases)",
+ ),
+ "dt_calc_all_matrix": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="DT Calc All Matrix",
+ description="Flag for whether to generate a heatmap for all samples together",
+ ),
+ "min_frip_overlap": NextflowParameter(
+ type=Optional[float],
+ default=0.2,
+ section_title=None,
+ display_name="Min FRiP Overlap",
+ description="Minimum fragment overlap for FriP score",
+ ),
+ "min_peak_overlap": NextflowParameter(
+ type=Optional[float],
+ default=0.2,
+ section_title=None,
+ display_name="Min Peak Overlap",
+ description="Minimum peak overlap for peak reproducibility plot",
+ ),
+ "igv_sort_by_groups": NextflowParameter(
+ type=bool,
+ default=True,
+ section_title=None,
+ display_name="IGV Sort by Groups",
+ description="Sort the IGV output tracks by group",
+ ),
+ "singularity_pull_docker_container": NextflowParameter(
+ type=bool,
+ default=None,
+ section_title=None,
+ display_name="Singularity Pull Docker Container",
+ description="Pull Docker container.",
+ ),
+ "multiqc_methods_description": NextflowParameter(
+ type=Optional[str],
+ default=None,
+ section_title=None,
+ display_name="MultiQC Methods Description",
+ description="Custom MultiQC yaml file containing HTML including a methods description.",
+ ),
+}
diff --git a/version b/version
new file mode 100644
index 00000000..be94e6f5
--- /dev/null
+++ b/version
@@ -0,0 +1 @@
+3.2.2
diff --git a/wf/__init__.py b/wf/__init__.py
new file mode 100644
index 00000000..cee09a9e
--- /dev/null
+++ b/wf/__init__.py
@@ -0,0 +1,353 @@
+from typing import List, Optional
+
+from latch.resources.launch_plan import LaunchPlan
+from latch.resources.workflow import workflow
+from latch.types import metadata
+from latch.types.directory import LatchDir, LatchOutputDir
+from latch.types.file import LatchFile
+
+from wf.entrypoint import Reference, SampleSheet, initialize, nextflow_runtime
+
+
+@workflow(metadata._nextflow_metadata)
+def nf_nf_core_cutandrun(
+ input: List[SampleSheet],
+ multiqc_title: Optional[str],
+ save_reference: bool,
+ save_merged_fastq: bool,
+ save_trimmed: bool,
+ save_spikein_aligned: bool,
+ save_unaligned: bool,
+ save_align_intermed: bool,
+ email: Optional[str],
+ dump_scale_factors: bool,
+ genome_source: str,
+ genome: Optional[str],
+ latch_genome: Optional[Reference],
+ bowtie2: Optional[LatchDir],
+ gtf: Optional[LatchFile],
+ gene_bed: Optional[LatchFile],
+ blacklist: Optional[LatchFile],
+ spikein_bowtie2: Optional[LatchFile],
+ spikein_fasta: Optional[LatchFile],
+ fasta: Optional[LatchFile],
+ only_input: bool,
+ only_genome: bool,
+ only_preqc: bool,
+ only_alignment: bool,
+ only_filtering: bool,
+ only_peak_calling: bool,
+ skip_fastqc: bool,
+ skip_trimming: bool,
+ skip_removeduplicates: bool,
+ skip_reporting: bool,
+ skip_preseq: bool,
+ skip_igv: bool,
+ skip_dt_qc: bool,
+ skip_heatmaps: bool,
+ skip_peak_qc: bool,
+ skip_multiqc: bool,
+ remove_mitochondrial_reads: bool,
+ run_name: str,
+ mito_name: Optional[str],
+ dedup_target_reads: bool,
+ remove_linear_duplicates: bool,
+ macs2_pvalue: Optional[float],
+ singularity_pull_docker_container: bool,
+ multiqc_methods_description: Optional[str],
+ spikein_genome: Optional[str] = "K12-MG1655",
+ clip_r1: Optional[int] = 0,
+ clip_r2: Optional[int] = 0,
+ three_prime_clip_r1: Optional[int] = 0,
+ three_prime_clip_r2: Optional[int] = 0,
+ trim_nextseq: Optional[int] = 0,
+ minimum_alignment_q_score: Optional[int] = 20,
+ end_to_end: bool = True,
+ normalisation_mode: Optional[str] = "Spikein",
+ normalisation_binsize: Optional[int] = 50,
+ peakcaller: Optional[str] = "seacr",
+ use_control: bool = True,
+ extend_fragments: bool = True,
+ igg_scale_factor: Optional[float] = 0.5,
+ seacr_peak_threshold: Optional[float] = 0.05,
+ seacr_norm: Optional[str] = "non",
+ seacr_stringent: Optional[str] = "stringent",
+ macs2_qvalue: Optional[float] = 0.01,
+ macs_gsize: Optional[float] = 2700000000.0,
+ macs2_narrow_peak: bool = True,
+ macs2_broad_cutoff: Optional[float] = 0.1,
+ consensus_peak_mode: Optional[str] = "group",
+ replicate_threshold: Optional[float] = 1.0,
+ igv_show_gene_names: bool = True,
+ dt_qc_bam_binsize: Optional[int] = 500,
+ dt_qc_corr_method: Optional[str] = "pearson",
+ dt_heatmap_gene_beforelen: Optional[int] = 3000,
+ dt_heatmap_gene_bodylen: Optional[int] = 5000,
+ dt_heatmap_gene_afterlen: Optional[int] = 3000,
+ dt_heatmap_peak_beforelen: Optional[int] = 3000,
+ dt_heatmap_peak_afterlen: Optional[int] = 3000,
+ dt_calc_all_matrix: bool = True,
+ min_frip_overlap: Optional[float] = 0.2,
+ min_peak_overlap: Optional[float] = 0.2,
+ igv_sort_by_groups: bool = True,
+ outdir: LatchOutputDir = LatchOutputDir("latch:///CutandRun"),
+) -> None:
+ """
+ nf-core/cutandrun is a best-practice bioinformatic analysis pipeline for CUT&RUN, CUT&Tag, and TIPseq experimental protocols that were developed to study protein-DNA interactions and epigenomic profiling.
+
+
+
+ 
+
+
+
+
+ Latch Verified
+
+
+
+
+
+ [](https://doi.org/10.5281/zenodo.5653535)
+
+ **nf-core/cutandrun** is a best-practice bioinformatic analysis pipeline for CUT&RUN, CUT&Tag, and TIPseq experimental protocols that were developed to study protein-DNA interactions and epigenomic profiling.
+
+ [CUT&RUN](https://elifesciences.org/articles/46314)
+
+ > Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019). Improved CUT&RUN chromatin profiling tools. _eLife_, _8_. https://doi.org/10.7554/eLife.46314
+
+ [CUT&Tag](https://www.nature.com/articles/s41467-019-09982-5)
+
+ > Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. _Nature Communications_, _10_(1), 1930. https://doi.org/10.1038/s41467-019-09982-5]
+
+ [TIPseq](https://rupress.org/jcb/article/220/12/e202103078/212821)
+
+ > Bartlett, D. A., Dileep, V., Handa, T., Ohkawa, Y., Kimura, H., Henikoff, S., & Gilbert, D. M. (2021). High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). Journal of Cell Biology, 220(12), e202103078. https://doi.org/10.1083/jcb.202103078
+
+ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a portable, reproducible manner. It is capable of using containerisation and package management making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process, which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules).
+
+ This workflow is hosted on Latch Workflows, using a native Nextflow integration, with a graphical interface for accessible analysis by scientists. There is also an integration with Latch Registry so that batched workflows can be launched from “graphical sample sheets” or tables associating raw sequencing files with metadata.
+
+ ## Pipeline summary
+
+ 1. Check input files
+ 2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
+ 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+ 4. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
+ 5. Alignment to both target and spike-in genomes ([`Bowtie 2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
+ 6. Filter on quality, sort and index alignments ([`samtools`](https://sourceforge.net/projects/samtools/files/samtools/))
+ 7. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/))
+ 8. Create bedGraph files ([`bedtools`](https://github.com/arq5x/bedtools2/)
+ 9. Create bigWig coverage files ([`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
+ 10. Peak calling ([`SEACR`](https://github.com/FredHutch/SEACR), [`MACS2`](https://github.com/macs3-project/MACS))
+ 11. Consensus peak merging and reporting ([`bedtools`](https://github.com/arq5x/bedtools2/))
+ 12. Library complexity ([preseq]([Preseq | The Smith Lab](http://smithlabresearch.org/software/preseq)))
+ 13. Fragment-based quality control ([`deepTools`](https://github.com/deeptools/deepTools/))
+ 14. Peak-based quality control ([`bedtools`](https://github.com/arq5x/bedtools2/), custom python)
+ 15. Heatmap peak analysis ([`deepTools`](https://github.com/deeptools/deepTools/))
+ 16. Genome browser session ([`IGV`](https://software.broadinstitute.org/software/igv/))
+ 17. Present all QC in web-based report ([`MultiQC`](http://multiqc.info/))
+
+ ## Usage
+
+ First, prepare a samplesheet with your input data that looks as follows:
+
+ `samplesheet.csv`:
+
+ ```
+ group,replicate,fastq_1,fastq_2,control
+ h3k27me3,1,h3k27me3_rep1_r1.fastq.gz,h3k27me3_rep1_r2.fastq.gz,igg_ctrl
+ h3k27me3,2,h3k27me3_rep2_r1.fastq.gz,h3k27me3_rep2_r2.fastq.gz,igg_ctrl
+ igg_ctrl,1,igg_rep1_r1.fastq.gz,igg_rep1_r2.fastq.gz,
+ igg_ctrl,2,igg_rep2_r1.fastq.gz,igg_rep2_r2.fastq.gz,
+ ```
+
+ Each row represents a pair of fastq files (paired end).
+
+ ## Pipeline output
+
+ To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/cutandrun/results) tab on the nf-core website pipeline page.
+ For more details about the output files and reports, please refer to the
+ [output documentation](https://nf-co.re/cutandrun/output).
+
+ ## Credits
+
+ nf-core/cutandrun was originally written by Chris Cheshire ([@chris-cheshire](https://github.com/chris-cheshire)) and Charlotte West ([@charlotte-west](https://github.com/charlotte-west)) from [Luscombe Lab](https://www.crick.ac.uk/research/labs/nicholas-luscombe) at [The Francis Crick Institute](https://www.crick.ac.uk/), London, UK.
+
+ The pipeline structure and parts of the downstream analysis were adapted from the original CUT&Tag analysis [protocol](https://yezhengstat.github.io/CUTTag_tutorial/) from the [Henikoff Lab](https://research.fredhutch.org/henikoff/en.html). The removal of duplicates arising from linear amplification (also known as T7 duplicates) in the TIPseq protocol was implemented as described in the original [TIPseq paper](https://rupress.org/jcb/article/220/12/e202103078/212821).
+
+ We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and everyone in the Luscombe Lab ([@luslab](https://github.com/luslab)) for their extensive assistance in the development of this pipeline.
+
+ ](docs/images/crick_logo.png)
+
+ ## Contributions and Support
+
+ If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+
+ For further information or help, don't hesitate to get in touch on the [Slack `#cutandrun` channel](https://nfcore.slack.com/channels/cutandrun) (you can join with [this invite](https://nf-co.re/join/slack)).
+
+ ## Citations
+
+ If you use nf-core/cutandrun for your analysis, please cite it using the following doi: [10.5281/zenodo.5653535](https://doi.org/10.5281/zenodo.5653535)
+
+ An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
+ You can cite the `nf-core` publication as follows:
+
+ > **The nf-core framework for community-curated bioinformatics pipelines.**
+ >
+ > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+ >
+ > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+
+ """
+
+ pvc_name: str = initialize(run_name=run_name)
+ nextflow_runtime(
+ pvc_name=pvc_name,
+ input=input,
+ outdir=outdir,
+ multiqc_title=multiqc_title,
+ save_reference=save_reference,
+ save_merged_fastq=save_merged_fastq,
+ save_trimmed=save_trimmed,
+ save_spikein_aligned=save_spikein_aligned,
+ save_unaligned=save_unaligned,
+ save_align_intermed=save_align_intermed,
+ email=email,
+ dump_scale_factors=dump_scale_factors,
+ genome=genome,
+ genome_source=genome_source,
+ latch_genome=latch_genome,
+ bowtie2=bowtie2,
+ gtf=gtf,
+ gene_bed=gene_bed,
+ blacklist=blacklist,
+ spikein_genome=spikein_genome,
+ spikein_bowtie2=spikein_bowtie2,
+ spikein_fasta=spikein_fasta,
+ fasta=fasta,
+ only_input=only_input,
+ only_genome=only_genome,
+ only_preqc=only_preqc,
+ only_alignment=only_alignment,
+ only_filtering=only_filtering,
+ only_peak_calling=only_peak_calling,
+ skip_fastqc=skip_fastqc,
+ skip_trimming=skip_trimming,
+ skip_removeduplicates=skip_removeduplicates,
+ skip_reporting=skip_reporting,
+ skip_preseq=skip_preseq,
+ skip_igv=skip_igv,
+ skip_dt_qc=skip_dt_qc,
+ skip_heatmaps=skip_heatmaps,
+ skip_peak_qc=skip_peak_qc,
+ skip_multiqc=skip_multiqc,
+ clip_r1=clip_r1,
+ clip_r2=clip_r2,
+ three_prime_clip_r1=three_prime_clip_r1,
+ three_prime_clip_r2=three_prime_clip_r2,
+ trim_nextseq=trim_nextseq,
+ minimum_alignment_q_score=minimum_alignment_q_score,
+ remove_mitochondrial_reads=remove_mitochondrial_reads,
+ run_name=run_name,
+ mito_name=mito_name,
+ dedup_target_reads=dedup_target_reads,
+ remove_linear_duplicates=remove_linear_duplicates,
+ end_to_end=end_to_end,
+ normalisation_mode=normalisation_mode,
+ normalisation_binsize=normalisation_binsize,
+ peakcaller=peakcaller,
+ use_control=use_control,
+ extend_fragments=extend_fragments,
+ igg_scale_factor=igg_scale_factor,
+ seacr_peak_threshold=seacr_peak_threshold,
+ seacr_norm=seacr_norm,
+ seacr_stringent=seacr_stringent,
+ macs2_qvalue=macs2_qvalue,
+ macs2_pvalue=macs2_pvalue,
+ macs_gsize=macs_gsize,
+ macs2_narrow_peak=macs2_narrow_peak,
+ macs2_broad_cutoff=macs2_broad_cutoff,
+ consensus_peak_mode=consensus_peak_mode,
+ replicate_threshold=replicate_threshold,
+ igv_show_gene_names=igv_show_gene_names,
+ dt_qc_bam_binsize=dt_qc_bam_binsize,
+ dt_qc_corr_method=dt_qc_corr_method,
+ dt_heatmap_gene_beforelen=dt_heatmap_gene_beforelen,
+ dt_heatmap_gene_bodylen=dt_heatmap_gene_bodylen,
+ dt_heatmap_gene_afterlen=dt_heatmap_gene_afterlen,
+ dt_heatmap_peak_beforelen=dt_heatmap_peak_beforelen,
+ dt_heatmap_peak_afterlen=dt_heatmap_peak_afterlen,
+ dt_calc_all_matrix=dt_calc_all_matrix,
+ min_frip_overlap=min_frip_overlap,
+ min_peak_overlap=min_peak_overlap,
+ igv_sort_by_groups=igv_sort_by_groups,
+ singularity_pull_docker_container=singularity_pull_docker_container,
+ multiqc_methods_description=multiqc_methods_description,
+ )
+
+
+LaunchPlan(
+ nf_nf_core_cutandrun,
+ "Test Data",
+ {
+ "input": [
+ SampleSheet(
+ group="h3k27me3",
+ replicate=1,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k27me3_rep1_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k27me3_rep1_r2.fastq.gz"),
+ control="igg",
+ ),
+ SampleSheet(
+ group="h3k27me3",
+ replicate=2,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k27me3_rep2_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k27me3_rep2_r2.fastq.gz"),
+ control="igg",
+ ),
+ SampleSheet(
+ group="h3k4me3",
+ replicate=1,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k4me3_rep1_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k4me3_rep1_r2.fastq.gz"),
+ control="igg",
+ ),
+ SampleSheet(
+ group="h3k4me3",
+ replicate=2,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k4me3_rep2_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/h3k4me3_rep2_r2.fastq.gz"),
+ control="igg",
+ ),
+ SampleSheet(
+ group="igg",
+ replicate=1,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/igg_rep1_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/igg_rep1_r2.fastq.gz"),
+ control=None,
+ ),
+ SampleSheet(
+ group="igg",
+ replicate=2,
+ fastq_1=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/igg_rep2_r1.fastq.gz"),
+ fastq_2=LatchFile("s3://latch-public/test-data/35729/cutandrun/test_data/igg_rep2_r2.fastq.gz"),
+ control=None,
+ ),
+ ],
+ "blacklist": LatchFile("s3://latch-public/test-data/35729/cutandrun/hg38-blacklist.bed"),
+ "spikein_bowtie2": LatchFile("s3://latch-public/test-data/35729/cutandrun/e_coli_U00096_3.tar.gz"),
+ "spikein_fasta": LatchFile("s3://latch-public/test-data/35729/cutandrun/e_coli_U00096_3.fa"),
+ "genome_source": "input_ref",
+ "fasta": LatchFile("s3://latch-public/test-data/35729/cutandrun/hg38-chr20.fa"),
+ "bowtie2": LatchDir("s3://latch-public/test-data/35729/cutandrun/hg38-chr20-bowtie2/"),
+ "gtf": LatchFile("s3://latch-public/test-data/35729/cutandrun/hg38-chr20-genes.gtf"),
+ "gene_bed": LatchFile("s3://latch-public/test-data/35729/cutandrun/hg38-chr20-genes.bed"),
+ "run_name": "Test_Run",
+ "peakcaller": "seacr",
+ "mito_name": "chrM",
+ "remove_linear_duplicates": True,
+ "remove_mitochondrial_reads": True,
+ },
+)
diff --git a/wf/entrypoint.py b/wf/entrypoint.py
new file mode 100644
index 00000000..a2fd7e24
--- /dev/null
+++ b/wf/entrypoint.py
@@ -0,0 +1,339 @@
+import os
+import shutil
+import subprocess
+import sys
+from dataclasses import dataclass
+from enum import Enum
+from pathlib import Path
+from typing import List, Optional
+
+import requests
+from latch.executions import rename_current_execution, report_nextflow_used_storage
+from latch.ldata.path import LPath
+from latch.resources.tasks import custom_task, nextflow_runtime_task
+from latch.types import metadata
+from latch.types.directory import LatchDir, LatchOutputDir
+from latch.types.file import LatchFile
+from latch_cli.nextflow.utils import _get_execution_name
+from latch_cli.nextflow.workflow import get_flag
+from latch_cli.services.register.utils import import_module_by_path
+from latch_cli.utils import urljoins
+
+sys.stdout.reconfigure(line_buffering=True)
+
+meta = Path("latch_metadata") / "__init__.py"
+import_module_by_path(meta)
+
+
+@custom_task(cpu=0.25, memory=0.5, storage_gib=1)
+def initialize(run_name: str) -> str:
+ rename_current_execution(str(run_name))
+
+ token = os.environ.get("FLYTE_INTERNAL_EXECUTION_ID")
+ if token is None:
+ raise RuntimeError("failed to get execution token")
+
+ headers = {"Authorization": f"Latch-Execution-Token {token}"}
+
+ print("Provisioning shared storage volume... ", end="")
+ resp = requests.post(
+ "http://nf-dispatcher-service.flyte.svc.cluster.local/provision-storage-ofs",
+ headers=headers,
+ json={
+ "storage_expiration_hours": 1,
+ "version": 2,
+ },
+ )
+ resp.raise_for_status()
+ print("Done.")
+
+ return resp.json()["name"]
+
+
+@dataclass
+class SampleSheet:
+ group: str
+ replicate: int
+ fastq_1: LatchFile
+ fastq_2: LatchFile
+ control: Optional[str]
+
+
+class Reference(Enum):
+ hg38 = "GRCh38 (Homo Sapiens hg38)"
+ hg19 = "GRCh37 (Homo Sapiens hg19)"
+
+
+input_construct_samplesheet = metadata._nextflow_metadata.parameters["input"].samplesheet_constructor
+
+
+@nextflow_runtime_task(cpu=4, memory=8, storage_gib=100)
+def nextflow_runtime(
+ pvc_name: str,
+ input: List[SampleSheet],
+ outdir: LatchOutputDir,
+ multiqc_title: Optional[str],
+ save_reference: bool,
+ save_merged_fastq: bool,
+ save_trimmed: bool,
+ save_spikein_aligned: bool,
+ save_unaligned: bool,
+ save_align_intermed: bool,
+ email: Optional[str],
+ dump_scale_factors: bool,
+ genome_source: str,
+ genome: Optional[str],
+ latch_genome: Optional[Reference],
+ bowtie2: Optional[LatchDir],
+ gtf: Optional[LatchFile],
+ gene_bed: Optional[LatchFile],
+ blacklist: Optional[LatchFile],
+ spikein_bowtie2: Optional[LatchFile],
+ spikein_fasta: Optional[LatchFile],
+ fasta: Optional[LatchFile],
+ only_input: bool,
+ only_genome: bool,
+ only_preqc: bool,
+ only_alignment: bool,
+ only_filtering: bool,
+ only_peak_calling: bool,
+ skip_fastqc: bool,
+ skip_trimming: bool,
+ skip_removeduplicates: bool,
+ skip_reporting: bool,
+ skip_preseq: bool,
+ skip_igv: bool,
+ skip_dt_qc: bool,
+ skip_heatmaps: bool,
+ skip_peak_qc: bool,
+ skip_multiqc: bool,
+ remove_mitochondrial_reads: bool,
+ run_name: str,
+ mito_name: Optional[str],
+ dedup_target_reads: bool,
+ remove_linear_duplicates: bool,
+ macs2_pvalue: Optional[float],
+ singularity_pull_docker_container: bool,
+ multiqc_methods_description: Optional[str],
+ spikein_genome: Optional[str],
+ clip_r1: Optional[int],
+ clip_r2: Optional[int],
+ three_prime_clip_r1: Optional[int],
+ three_prime_clip_r2: Optional[int],
+ trim_nextseq: Optional[int],
+ minimum_alignment_q_score: Optional[int],
+ end_to_end: bool,
+ normalisation_mode: Optional[str],
+ normalisation_binsize: Optional[int],
+ peakcaller: Optional[str],
+ use_control: bool,
+ extend_fragments: bool,
+ igg_scale_factor: Optional[float],
+ seacr_peak_threshold: Optional[float],
+ seacr_norm: Optional[str],
+ seacr_stringent: Optional[str],
+ macs2_qvalue: Optional[float],
+ macs_gsize: Optional[float],
+ macs2_narrow_peak: bool,
+ macs2_broad_cutoff: Optional[float],
+ consensus_peak_mode: Optional[str],
+ replicate_threshold: Optional[float],
+ igv_show_gene_names: bool,
+ dt_qc_bam_binsize: Optional[int],
+ dt_qc_corr_method: Optional[str],
+ dt_heatmap_gene_beforelen: Optional[int],
+ dt_heatmap_gene_bodylen: Optional[int],
+ dt_heatmap_gene_afterlen: Optional[int],
+ dt_heatmap_peak_beforelen: Optional[int],
+ dt_heatmap_peak_afterlen: Optional[int],
+ dt_calc_all_matrix: bool,
+ min_frip_overlap: Optional[float],
+ min_peak_overlap: Optional[float],
+ igv_sort_by_groups: bool,
+) -> None:
+ shared_dir = Path("/nf-workdir")
+
+ input_samplesheet = input_construct_samplesheet(input)
+
+ ignore_list = [
+ "latch",
+ ".latch",
+ ".git",
+ "nextflow",
+ ".nextflow",
+ "work",
+ "results",
+ "miniconda",
+ "anaconda3",
+ "mambaforge",
+ ]
+
+ shutil.copytree(
+ Path("/root"),
+ shared_dir,
+ ignore=lambda src, names: ignore_list,
+ ignore_dangling_symlinks=True,
+ dirs_exist_ok=True,
+ )
+
+ if genome_source == "latch_genome_source":
+ fasta = os.path.join(
+ "s3://latch-public/test-data/35729/cutandrun/",
+ latch_genome.name,
+ latch_genome.name + ".fa",
+ )
+ gtf = os.path.join(
+ "s3://latch-public/test-data/35729/cutandrun/",
+ latch_genome.name,
+ latch_genome.name + ".refGene.gtf",
+ )
+ bowtie2 = os.path.join("s3://latch-public/test-data/35729/cutandrun/", latch_genome.name, "bowtie2")
+
+ cmd = [
+ "/root/nextflow",
+ "run",
+ str(shared_dir / "main.nf"),
+ "-work-dir",
+ str(shared_dir),
+ "-profile",
+ "docker",
+ "-c",
+ "latch.config",
+ "-resume",
+ *get_flag("input", input_samplesheet),
+ *get_flag("outdir", LatchOutputDir(outdir.remote_path + "/" + run_name)),
+ *get_flag("multiqc_title", multiqc_title),
+ *get_flag("save_reference", save_reference),
+ *get_flag("save_merged_fastq", save_merged_fastq),
+ *get_flag("save_trimmed", save_trimmed),
+ *get_flag("save_spikein_aligned", save_spikein_aligned),
+ *get_flag("save_unaligned", save_unaligned),
+ *get_flag("save_align_intermed", save_align_intermed),
+ *get_flag("email", email),
+ *get_flag("dump_scale_factors", dump_scale_factors),
+ *get_flag("genome", genome),
+ *get_flag("bowtie2", bowtie2),
+ *get_flag("gtf", gtf),
+ *get_flag("gene_bed", gene_bed),
+ *get_flag("blacklist", blacklist),
+ *get_flag("spikein_genome", spikein_genome),
+ *get_flag("spikein_bowtie2", spikein_bowtie2),
+ *get_flag("spikein_fasta", spikein_fasta),
+ *get_flag("fasta", fasta),
+ *get_flag("only_input", only_input),
+ *get_flag("only_genome", only_genome),
+ *get_flag("only_preqc", only_preqc),
+ *get_flag("only_alignment", only_alignment),
+ *get_flag("only_filtering", only_filtering),
+ *get_flag("only_peak_calling", only_peak_calling),
+ *get_flag("skip_fastqc", skip_fastqc),
+ *get_flag("skip_trimming", skip_trimming),
+ *get_flag("skip_removeduplicates", skip_removeduplicates),
+ *get_flag("skip_reporting", skip_reporting),
+ *get_flag("skip_preseq", skip_preseq),
+ *get_flag("skip_igv", skip_igv),
+ *get_flag("skip_dt_qc", skip_dt_qc),
+ *get_flag("skip_heatmaps", skip_heatmaps),
+ *get_flag("skip_peak_qc", skip_peak_qc),
+ *get_flag("skip_multiqc", skip_multiqc),
+ *get_flag("clip_r1", clip_r1),
+ *get_flag("clip_r2", clip_r2),
+ *get_flag("three_prime_clip_r1", three_prime_clip_r1),
+ *get_flag("three_prime_clip_r2", three_prime_clip_r2),
+ *get_flag("trim_nextseq", trim_nextseq),
+ *get_flag("minimum_alignment_q_score", minimum_alignment_q_score),
+ *get_flag("remove_mitochondrial_reads", remove_mitochondrial_reads),
+ *get_flag("mito_name", mito_name),
+ *get_flag("dedup_target_reads", dedup_target_reads),
+ *get_flag("remove_linear_duplicates", remove_linear_duplicates),
+ *get_flag("end_to_end", end_to_end),
+ *get_flag("normalisation_mode", normalisation_mode),
+ *get_flag("normalisation_binsize", normalisation_binsize),
+ *get_flag("peakcaller", peakcaller),
+ *get_flag("use_control", use_control),
+ *get_flag("extend_fragments", extend_fragments),
+ *get_flag("igg_scale_factor", igg_scale_factor),
+ *get_flag("seacr_peak_threshold", seacr_peak_threshold),
+ *get_flag("seacr_norm", seacr_norm),
+ *get_flag("seacr_stringent", seacr_stringent),
+ *get_flag("macs2_qvalue", macs2_qvalue),
+ *get_flag("macs2_pvalue", macs2_pvalue),
+ *get_flag("macs_gsize", macs_gsize),
+ *get_flag("macs2_narrow_peak", macs2_narrow_peak),
+ *get_flag("macs2_broad_cutoff", macs2_broad_cutoff),
+ *get_flag("consensus_peak_mode", consensus_peak_mode),
+ *get_flag("replicate_threshold", replicate_threshold),
+ *get_flag("igv_show_gene_names", igv_show_gene_names),
+ *get_flag("dt_qc_bam_binsize", dt_qc_bam_binsize),
+ *get_flag("dt_qc_corr_method", dt_qc_corr_method),
+ *get_flag("dt_heatmap_gene_beforelen", dt_heatmap_gene_beforelen),
+ *get_flag("dt_heatmap_gene_bodylen", dt_heatmap_gene_bodylen),
+ *get_flag("dt_heatmap_gene_afterlen", dt_heatmap_gene_afterlen),
+ *get_flag("dt_heatmap_peak_beforelen", dt_heatmap_peak_beforelen),
+ *get_flag("dt_heatmap_peak_afterlen", dt_heatmap_peak_afterlen),
+ *get_flag("dt_calc_all_matrix", dt_calc_all_matrix),
+ *get_flag("min_frip_overlap", min_frip_overlap),
+ *get_flag("min_peak_overlap", min_peak_overlap),
+ *get_flag("igv_sort_by_groups", igv_sort_by_groups),
+ *get_flag("singularity_pull_docker_container", singularity_pull_docker_container),
+ *get_flag("multiqc_methods_description", multiqc_methods_description),
+ ]
+
+ print("Launching Nextflow Runtime")
+ print(" ".join(cmd))
+ print(flush=True)
+
+ failed = False
+ try:
+ env = {
+ **os.environ,
+ "NXF_ANSI_LOG": "false",
+ "NXF_HOME": "/root/.nextflow",
+ "NXF_OPTS": "-Xms1536M -Xmx6144M -XX:ActiveProcessorCount=4",
+ "NXF_DISABLE_CHECK_LATEST": "true",
+ "NXF_ENABLE_VIRTUAL_THREADS": "false",
+ }
+ subprocess.run(
+ cmd,
+ env=env,
+ check=True,
+ cwd=str(shared_dir),
+ )
+ except subprocess.CalledProcessError:
+ failed = True
+ finally:
+ print()
+
+ nextflow_log = shared_dir / ".nextflow.log"
+ if nextflow_log.exists():
+ name = _get_execution_name()
+ if name is None:
+ print("Skipping logs upload, failed to get execution name")
+ else:
+ remote = LPath(urljoins("latch:///your_log_dir/nf_nf_core_cutandrun", name, "nextflow.log"))
+ print(f"Uploading .nextflow.log to {remote.path}")
+ remote.upload_from(nextflow_log)
+
+ print("Computing size of workdir... ", end="")
+ try:
+ result = subprocess.run(
+ ["du", "-sb", str(shared_dir)],
+ check=True,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ text=True,
+ timeout=5 * 60,
+ )
+
+ size = int(result.stdout.split()[0])
+ report_nextflow_used_storage(size)
+ print(f"Done. Workdir size: {size / 1024 / 1024 / 1024: .2f} GiB")
+ except subprocess.TimeoutExpired:
+ print("Failed to compute storage size: Operation timed out after 5 minutes.")
+ except subprocess.CalledProcessError as e:
+ print(f"Failed to compute storage size: {e.stderr}")
+ except Exception as e:
+ print(f"Failed to compute storage size: {e}")
+
+ if failed:
+ sys.exit(1)