From 8adc7cc3df18971e3e3b9c694f54bb1b5c8780ec Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Fri, 29 Sep 2023 11:16:37 -0400
Subject: [PATCH 01/26] fix: scratch path update, log file dir update

---
 workflow/scripts/_spooker | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflow/scripts/_spooker b/workflow/scripts/_spooker
index d772359..9d2fd8a 100644
--- a/workflow/scripts/_spooker
+++ b/workflow/scripts/_spooker
@@ -35,10 +35,10 @@ if [[ $ISBIOWULF == true || $ISFRCE == true ]];then
 	    fi
         fi
         echo "spook is now in PATH:$SPOOK"
-        SPOOK_COPY2DIR="/scratch/carlisle"
+        SPOOK_COPY2DIR="/scratch/ccbrpipeliner"
     fi
     if [[ $ISFRCE == true ]];then
-        SPOOK_COPY2DIR="/mnt/projects/CCBR-Pipelines/pipelines/userdata/carlisle"
+        SPOOK_COPY2DIR="/mnt/projects/CCBR-Pipelines/pipelines/userdata/ccbrpipeliner"
     fi
 
     DT=$(date +%y%m%d%H%M%S)
@@ -63,8 +63,8 @@ if [[ $ISBIOWULF == true || $ISFRCE == true ]];then
         tree $PIPELINE_OUTDIR >> $treefile
         cmd="$cmd $treefile"
 
-        if [[ -d "${PIPELINE_OUTDIR}/logfiles" ]];then
-            logdir="${PIPELINE_OUTDIR}/logfiles"
+        if [[ -d "${PIPELINE_OUTDIR}/logs" ]];then
+            logdir="${PIPELINE_OUTDIR}/logs"
             for thisfile in "snakemake.log" "snakemake.log.jobby" "master.log" "runtime_statistics.json";do
                 absthisfile="${logdir}/${thisfile}"
                 if [[ -f "$absthisfile" ]];then

From 10967f45fb66eba463eaff5673d711578cb5fba0 Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Mon, 16 Oct 2023 12:32:47 -0400
Subject: [PATCH 02/26] run all rules

---
 workflow/Snakefile | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 1669890..1cc9346 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -197,30 +197,30 @@ rule all:
         # ALIGN / deeptools_heatmap
         unpack(run_deeptools_heatmap),
 
-        # # ALIGN / create_library_norm_scales
-        # unpack(run_library_norm),
+        # ALIGN / create_library_norm_scales
+        unpack(run_library_norm),
 
-        # # ALIGN / alignstats
-        # expand(join(RESULTSDIR,"alignment_stats","{replicate}.alignment_stats.yaml"),replicate=REPLICATES),
+        # ALIGN / alignstats
+        expand(join(RESULTSDIR,"alignment_stats","{replicate}.alignment_stats.yaml"),replicate=REPLICATES),
         
-        # # ALIGN / gather_alignstats
-        # join(RESULTSDIR,"alignment_stats","alignment_stats.tsv"),
+        # ALIGN / gather_alignstats
+        join(RESULTSDIR,"alignment_stats","alignment_stats.tsv"),
 
-        # # PEAKCALLS / macs2_narrow, macs2_broad, seacr_stringent, seacr_relaxed, gopeaks_narrow, gopeaks_broad
-        # unpack(run_macs2),
-        # unpack(run_seacr),
-        # unpack(run_gopeaks),
+        # PEAKCALLS / macs2_narrow, macs2_broad, seacr_stringent, seacr_relaxed, gopeaks_narrow, gopeaks_broad
+        unpack(run_macs2),
+        unpack(run_seacr),
+        unpack(run_gopeaks),
 
-        # # QC
-        # unpack(run_qc),
+        # QC
+        unpack(run_qc),
 
-        # # DIFF / create_contrast_data_files
-        # unpack(run_contrasts),
+        # DIFF / create_contrast_data_files
+        unpack(run_contrasts),
         
-        # # ANNOTATION / findMotif, rose, create_contrast_peakcaller_files, go_enrichment
-        # unpack(get_motifs),
-        # unpack(get_rose),
-        # unpack(get_enrichment)
+        # ANNOTATION / findMotif, rose, create_contrast_peakcaller_files, go_enrichment
+        unpack(get_motifs),
+        unpack(get_rose),
+        unpack(get_enrichment)
 
 # create jobby tables
 ## command for jobby: bash scripts/_run_jobby_on_snakemake_log logs/snakemake.log _jobby.py | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short

From f79b1725fa16a84195672c4041bc1646448b2cb1 Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Mon, 16 Oct 2023 12:34:27 -0400
Subject: [PATCH 03/26] check for exact matches in configs

---
 carlisle | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/carlisle b/carlisle
index 7872439..175df12 100755
--- a/carlisle
+++ b/carlisle
@@ -194,8 +194,9 @@ function controlcheck(){
   check2=`awk '{print $2}' ${WORKDIR}/config/contrasts.tsv`
   
   for sample_id in ${control_list[@]}; do
-    if [[ $check1 =~ $sample_id || $check2 =~ $sample_id ]]; then 
+    if [[ $check1 == $sample_id || $check2 == $sample_id ]]; then 
       echo "Controls ($sample_id) cannot be listed in contrast.csv - update and re-run"
+      echo "$check1 okkk $check2"
       exit 0
     fi
   done

From 1005fa03f6ba406e6016288166540d6faf25f716 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Oct 2023 09:00:09 -0400
Subject: [PATCH 04/26] feat: create 'install' script

---
 install.sh | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100755 install.sh

diff --git a/install.sh b/install.sh
new file mode 100755
index 0000000..55b4aa9
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+# usage:
+#   ./install.sh new/path/to/install
+# examples
+#   ./install.sh .v2.4.0
+#   /data/CCBR_Pipeliner/Pipelines/CARLISLE/dev/install.sh /data/CCBR_Pipeliner/Pipelines/CARLISLE/.v2.5.0-a
+set -euo pipefail
+
+VERSION=$1
+mkdir -p ${VERSION}/bin
+INSTALL_PATH=$(readlink -f ${VERSION}/bin)
+DIRNAME=$(readlink -f $(dirname $0))
+
+if [ -n "$(ls -A $INSTALL_PATH 2>/dev/null)" ]
+then
+    echo "ERROR: directory not empty: ${INSTALL_PATH}"
+    echo $(ls $INSTALL_PATH)
+    exit 1
+fi
+
+# copy essential files & directories
+
+## carlisle CLI script
+cp $DIRNAME/carlisle $INSTALL_PATH/
+
+## all config & workflow scripts;
+for subdir in config workflow/scripts
+do  
+    mkdir -p ${INSTALL_PATH}/$subdir
+    cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
+done
+cp ${DIRNAME}/workflow/Snakefile ${INSTALL_PATH}/workflow
+
+## selected resources
+mkdir -p ${INSTALL_PATH}/resources/
+cp ${DIRNAME}/resources/*.yaml ${INSTALL_PATH}/resources/
+
+# export path
+if [[ ":$PATH:" != *":${INSTALL_PATH}:"* ]];then
+    export PATH="${PATH}:${INSTALL_PATH}"
+fi
+
+echo "${INSTALL_PATH}"

From 4f75a9783dc3965d755b075277d1f53d36efe76b Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Oct 2023 09:03:51 -0400
Subject: [PATCH 05/26] ci: run linter on PRs too

---
 .github/workflows/lintr.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml
index ab839dc..03da921 100644
--- a/.github/workflows/lintr.yaml
+++ b/.github/workflows/lintr.yaml
@@ -4,6 +4,11 @@ on:
     branches:
       - master
       - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
 jobs:
   Lintr:
     runs-on: ubuntu-latest
@@ -22,4 +27,4 @@ jobs:
         touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
         snakemake --lint -s /opt2/workflow/Snakefile \
         -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
-        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"
\ No newline at end of file
+        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"

From 698328042116cb5b4a98d98b3e4ca2e2c6e70720 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Oct 2023 09:07:07 -0400
Subject: [PATCH 06/26] ci: do a dryrun

---
 .github/workflows/test_dev.yml | 38 ++++++++++++++++++++++------------
 1 file changed, 25 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_dev.yml b/.github/workflows/test_dev.yml
index ed83aa9..4d08b34 100644
--- a/.github/workflows/test_dev.yml
+++ b/.github/workflows/test_dev.yml
@@ -1,25 +1,37 @@
-name: DevTesting
+name: test
 on:
   push:
     branches:
+      - master
       - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4.1.0
     - uses: docker://snakemake/snakemake:v7.19.1
       with:
         directory: '.test'
-    - name: Dev Testing Workflow
-      continue-on-error: true
+    - name: dryrun
+      shell: bash {0}
       run: |
-        docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
-          "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \
-          cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \
-          cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \
-          cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \
-          cd /opt2/output_carlisle/annotation && \
-          touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
-          snakemake --lint -s /opt2/workflow/Snakefile \
-          -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
-          echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"
+        # TODO: install & use `carlisle init` instead of manually copying files
+        mkdir output_carlisle
+        for dir in workflow workflow/scripts config resources
+        do 
+          cp -r $dir output_carlisle
+        done
+        mkdir output_carlisle/annotation
+        for f in hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa
+        do
+          touch output_carlisle/annotation/$f
+        done
+        # TODO: use `carlisle run --mode dryrun`
+        cd output_carlisle
+        docker run -v $PWD:/opt2/output_carlisle snakemake/snakemake:v7.19.1 /bin/bash -c \
+          "cd /opt2/output_carlisle && snakemake --dryrun --configfile .test/config_lint.yaml"

From 921f17bd659a7979d27641a6f721dd883f4c9c76 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Oct 2023 09:19:43 -0400
Subject: [PATCH 07/26] ci: action to add issues/PRs to personal project boards

---
 .github/workflows/projects.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 .github/workflows/projects.yml

diff --git a/.github/workflows/projects.yml b/.github/workflows/projects.yml
new file mode 100644
index 0000000..61a2816
--- /dev/null
+++ b/.github/workflows/projects.yml
@@ -0,0 +1,14 @@
+name: Add issues/PRs to user projects
+
+on:
+  issues:
+    types:
+      - assigned
+  pull_request:
+    types:
+      - assigned
+
+jobs:
+  add-to-project:
+    uses: CCBR/.github/.github/workflows/auto-add-user-project.yml@v0.1.0
+    secrets: inherit

From e2360c7853beedf732a48e34262c9affead528b3 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Oct 2023 14:28:12 -0400
Subject: [PATCH 08/26] fix: don't call module purge

or else it unloads ccbrpipeliner
---
 carlisle | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/carlisle b/carlisle
index 175df12..35b523a 100755
--- a/carlisle
+++ b/carlisle
@@ -14,7 +14,6 @@ SNAKEMAKE_VERSION="snakemake/7.19.1"
 SINGULARITY_VERSION="singularity/3.10.5"
 
 set -eo pipefail
-module purge
 
 SCRIPTNAME="$0"
 SCRIPTBASENAME=$(readlink -f $(basename $0))
@@ -443,4 +442,4 @@ function main(){
 }
 
 # call the main function
-main "$@"
\ No newline at end of file
+main "$@"

From af8c132c2c877e6e77f82619442157359d27b729 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Oct 2023 14:29:26 -0400
Subject: [PATCH 09/26] fix: copy annotation dir

---
 carlisle   | 2 +-
 install.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/carlisle b/carlisle
index 35b523a..6e0b37c 100755
--- a/carlisle
+++ b/carlisle
@@ -28,7 +28,7 @@ tools_specific_yaml="tools_biowulf.yaml"
 # these are relative to the workflows' base folder
 # these are copied into the WORKDIR
 ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml resources/cluster_* resources/tools_*"
-ESSENTIAL_FOLDERS="workflow/scripts"
+ESSENTIAL_FOLDERS="workflow/scripts annotation"
 # set extra singularity bindings
 EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/,/lscratch"
 
diff --git a/install.sh b/install.sh
index 55b4aa9..431a869 100755
--- a/install.sh
+++ b/install.sh
@@ -24,7 +24,7 @@ fi
 cp $DIRNAME/carlisle $INSTALL_PATH/
 
 ## all config & workflow scripts;
-for subdir in config workflow/scripts
+for subdir in config workflow/scripts annotation
 do  
     mkdir -p ${INSTALL_PATH}/$subdir
     cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir

From 57f7d79ff4bd5062ff776134d69346250328d148 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Oct 2023 14:31:32 -0400
Subject: [PATCH 10/26] fix: copy .test dir

---
 install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install.sh b/install.sh
index 431a869..976c916 100755
--- a/install.sh
+++ b/install.sh
@@ -24,7 +24,7 @@ fi
 cp $DIRNAME/carlisle $INSTALL_PATH/
 
 ## all config & workflow scripts;
-for subdir in config workflow/scripts annotation
+for subdir in config workflow/scripts annotation .test
 do  
     mkdir -p ${INSTALL_PATH}/$subdir
     cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir

From 6df550e59ab8986faea56c81d6dac8b85a318c04 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Oct 2023 14:42:38 -0400
Subject: [PATCH 11/26] fix: just copy the entire git repo dir during
 'installation'
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

🤷🏻‍♀️
---
 install.sh | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/install.sh b/install.sh
index 976c916..810e05b 100755
--- a/install.sh
+++ b/install.sh
@@ -18,22 +18,8 @@ then
     exit 1
 fi
 
-# copy essential files & directories
-
-## carlisle CLI script
-cp $DIRNAME/carlisle $INSTALL_PATH/
-
-## all config & workflow scripts;
-for subdir in config workflow/scripts annotation .test
-do  
-    mkdir -p ${INSTALL_PATH}/$subdir
-    cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
-done
-cp ${DIRNAME}/workflow/Snakefile ${INSTALL_PATH}/workflow
-
-## selected resources
-mkdir -p ${INSTALL_PATH}/resources/
-cp ${DIRNAME}/resources/*.yaml ${INSTALL_PATH}/resources/
+# copy entire repo, including dotfiles
+cp -r ${DIRNAME}/. ${INSTALL_PATH}
 
 # export path
 if [[ ":$PATH:" != *":${INSTALL_PATH}:"* ]];then

From 0041346c678010a79188eb0064d6f3289044c40e Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Oct 2023 14:50:43 -0400
Subject: [PATCH 12/26] fix: copy cluster-specific config & tool yaml files
 without wildcards

---
 carlisle | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/carlisle b/carlisle
index 6e0b37c..b5f8d30 100755
--- a/carlisle
+++ b/carlisle
@@ -27,7 +27,7 @@ tools_specific_yaml="tools_biowulf.yaml"
 # essential files
 # these are relative to the workflows' base folder
 # these are copied into the WORKDIR
-ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml resources/cluster_* resources/tools_*"
+ESSENTIAL_FILES="config/config.yaml config/samples.tsv config/contrasts.tsv config/fqscreen_config.conf config/multiqc_config.yaml"
 ESSENTIAL_FOLDERS="workflow/scripts annotation"
 # set extra singularity bindings
 EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/,/lscratch"
@@ -103,8 +103,8 @@ function init() {
   done
 
   # rename config dependent on partition used
-  cp $WORKDIR/config/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
-  cp $WORKDIR/config/$tools_specific_yaml $WORKDIR/config/tools.yaml
+  cp ${PIPELINE_HOME}/config/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
+  cp ${PIPELINE_HOME}/config/$tools_specific_yaml $WORKDIR/config/tools.yaml
 
   # copy essential folders
   for f in $ESSENTIAL_FOLDERS;do

From 25c0b1af20e6301b5bdebd64c994c3b6c1e6eeaa Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 08:27:03 -0400
Subject: [PATCH 13/26] fix: copy cluster/tool conf from resources

---
 carlisle | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/carlisle b/carlisle
index b5f8d30..37a50e0 100755
--- a/carlisle
+++ b/carlisle
@@ -103,8 +103,8 @@ function init() {
   done
 
   # rename config dependent on partition used
-  cp ${PIPELINE_HOME}/config/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
-  cp ${PIPELINE_HOME}/config/$tools_specific_yaml $WORKDIR/config/tools.yaml
+  cp ${PIPELINE_HOME}/resources/$cluster_specific_yaml $WORKDIR/config/cluster.yaml
+  cp ${PIPELINE_HOME}/resources/$tools_specific_yaml $WORKDIR/config/tools.yaml
 
   # copy essential folders
   for f in $ESSENTIAL_FOLDERS;do

From 01230a86dd928fd3fe1f07dc9182400295826776 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 08:27:19 -0400
Subject: [PATCH 14/26] Revert "fix: just copy the entire git repo dir during
 'installation'"

This reverts commit 6df550e59ab8986faea56c81d6dac8b85a318c04.
---
 install.sh | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/install.sh b/install.sh
index 810e05b..976c916 100755
--- a/install.sh
+++ b/install.sh
@@ -18,8 +18,22 @@ then
     exit 1
 fi
 
-# copy entire repo, including dotfiles
-cp -r ${DIRNAME}/. ${INSTALL_PATH}
+# copy essential files & directories
+
+## carlisle CLI script
+cp $DIRNAME/carlisle $INSTALL_PATH/
+
+## all config & workflow scripts;
+for subdir in config workflow/scripts annotation .test
+do  
+    mkdir -p ${INSTALL_PATH}/$subdir
+    cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
+done
+cp ${DIRNAME}/workflow/Snakefile ${INSTALL_PATH}/workflow
+
+## selected resources
+mkdir -p ${INSTALL_PATH}/resources/
+cp ${DIRNAME}/resources/*.yaml ${INSTALL_PATH}/resources/
 
 # export path
 if [[ ":$PATH:" != *":${INSTALL_PATH}:"* ]];then

From d4952ee7cd05c86cc9bf0320ab12ca348d0b1f60 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 09:10:04 -0400
Subject: [PATCH 15/26] refactor!: get version from installation path

VERSION will be blank if it doesn't match the semantic versioning format
https://semver.org/#is-there-a-suggested-regular-expression-regex-to-check-a-semver-string
---
 carlisle | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/carlisle b/carlisle
index 37a50e0..c24238f 100755
--- a/carlisle
+++ b/carlisle
@@ -32,24 +32,22 @@ ESSENTIAL_FOLDERS="workflow/scripts annotation"
 # set extra singularity bindings
 EXTRA_SINGULARITY_BINDS="-B /data/CCBR_Pipeliner/,/lscratch"
 
-function get_git_commitid_tag() {
-  # This function gets the latest git commit id and tag
-  # Input is PIPELINE_HOME folder which is a git folder
-    cd $1
-    gid=$(git rev-parse HEAD)
-    tag=$(git describe --tags $gid 2>/dev/null)
-    echo -ne "$gid\t$tag"
-}
-
 # ## setting PIPELINE_HOME
 PIPELINE_HOME=$(readlink -f $(dirname "$0"))
 echo "Pipeline Dir: $PIPELINE_HOME"
 # set snakefile
 SNAKEFILE="${PIPELINE_HOME}/workflow/Snakefile"
 
-# get github commit tag
-GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
-echo "Git Commit/Tag: $GIT_COMMIT_TAG"
+function get_version_from_path() {
+  PIPELINE_HOME=$1
+  VERSION="$(echo $PIPELINE_HOME | grep -oP 'v(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?' - )"
+  echo -ne $VERSION
+}
+
+# get version from directory name
+# regex source: https://semver.org/#is-there-a-suggested-regular-expression-regex-to-check-a-semver-string
+#echo "Version: $VERSION"
+echo "Version: $(get_version_from_path $PIPELINE_HOME)"
 
 function usage() { 
 # This function prints generic usage of the wrapper script.

From 852c79f40e0a013a3d7ed4cf7cf5ed5c455f28a1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 09:15:30 -0400
Subject: [PATCH 16/26] fix: recursively copy most directories

---
 install.sh | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/install.sh b/install.sh
index 976c916..59e7a29 100755
--- a/install.sh
+++ b/install.sh
@@ -24,16 +24,11 @@ fi
 cp $DIRNAME/carlisle $INSTALL_PATH/
 
 ## all config & workflow scripts;
-for subdir in config workflow/scripts annotation .test
+for subdir in annotation config workflow resources .test
 do  
     mkdir -p ${INSTALL_PATH}/$subdir
-    cp ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
+    cp -r ${DIRNAME}/$subdir/* ${INSTALL_PATH}/$subdir
 done
-cp ${DIRNAME}/workflow/Snakefile ${INSTALL_PATH}/workflow
-
-## selected resources
-mkdir -p ${INSTALL_PATH}/resources/
-cp ${DIRNAME}/resources/*.yaml ${INSTALL_PATH}/resources/
 
 # export path
 if [[ ":$PATH:" != *":${INSTALL_PATH}:"* ]];then

From 272e2622fd7478208721747ee5cf7d26e56c573f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 09:32:15 -0400
Subject: [PATCH 17/26] ci: use install script & carlisle init

---
 .github/workflows/test_dev.yml | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_dev.yml b/.github/workflows/test_dev.yml
index 4d08b34..5e27cb0 100644
--- a/.github/workflows/test_dev.yml
+++ b/.github/workflows/test_dev.yml
@@ -20,18 +20,8 @@ jobs:
     - name: dryrun
       shell: bash {0}
       run: |
-        # TODO: install & use `carlisle init` instead of manually copying files
-        mkdir output_carlisle
-        for dir in workflow workflow/scripts config resources
-        do 
-          cp -r $dir output_carlisle
-        done
-        mkdir output_carlisle/annotation
-        for f in hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa
-        do
-          touch output_carlisle/annotation/$f
-        done
+        bash ./install.sh ./carlisle-v9999.9999.9999-dev
+        ./carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./output_carlisle
         # TODO: use `carlisle run --mode dryrun`
-        cd output_carlisle
-        docker run -v $PWD:/opt2/output_carlisle snakemake/snakemake:v7.19.1 /bin/bash -c \
+        docker run -v ./output_carlisle:/opt2/output_carlisle snakemake/snakemake:v7.19.1 /bin/bash -c \
           "cd /opt2/output_carlisle && snakemake --dryrun --configfile .test/config_lint.yaml"

From e48957133ef61f62e21ae4d4c3ac0c74e47cc046 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 09:58:25 -0400
Subject: [PATCH 18/26] ci: make installed carlisle available to docker

---
 .github/workflows/test_dev.yml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test_dev.yml b/.github/workflows/test_dev.yml
index 5e27cb0..4bee8c1 100644
--- a/.github/workflows/test_dev.yml
+++ b/.github/workflows/test_dev.yml
@@ -20,8 +20,13 @@ jobs:
     - name: dryrun
       shell: bash {0}
       run: |
-        bash ./install.sh ./carlisle-v9999.9999.9999-dev
-        ./carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./output_carlisle
+        bash ./install.sh ./test-workdir/carlisle-v9999.9999.9999-dev
+        ./test-workdir/carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./test-workdir/output_carlisle
+        cp ./test-workdir/carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml ./test-workdir/output_carlisle/config/config.yaml
         # TODO: use `carlisle run --mode dryrun`
-        docker run -v ./output_carlisle:/opt2/output_carlisle snakemake/snakemake:v7.19.1 /bin/bash -c \
-          "cd /opt2/output_carlisle && snakemake --dryrun --configfile .test/config_lint.yaml"
+        docker run -v ./test-workdir/:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
+          "cd /opt2 && snakemake \
+            -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \
+            --dryrun \
+            --configfile .test/config_lint.yaml\
+            --workdir /opt2/test-workdir/output_carlisle"

From 82fd7cd3aba0f7206868c56df66237b437863ec8 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 19 Oct 2023 10:03:58 -0400
Subject: [PATCH 19/26] fix: directory snakemake arg

---
 .github/workflows/test_dev.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_dev.yml b/.github/workflows/test_dev.yml
index 4bee8c1..33a6a87 100644
--- a/.github/workflows/test_dev.yml
+++ b/.github/workflows/test_dev.yml
@@ -28,5 +28,5 @@ jobs:
           "cd /opt2 && snakemake \
             -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \
             --dryrun \
-            --configfile .test/config_lint.yaml\
-            --workdir /opt2/test-workdir/output_carlisle"
+            --configfile carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml \
+            --directory output_carlisle"

From 0fb95c25b079898517eaa686f102243ad06753c3 Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Mon, 8 Jan 2024 18:00:13 -0500
Subject: [PATCH 20/26] docs: adding citation file

---
 CITATION.cff | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..9ea2218
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use CARLISLE, please cite it as below."
+authors:
+- family-names: "Sevilla"
+  given-names: "Samantha"
+  orcid: "https://orcid.org/0000-0002-8734-9875"
+- family-names: "Koparde"
+  given-names: "Vishal"
+  orcid: "https://orcid.org/0000-0001-8978-8495"
+- family-names: "Chou"
+  given-names: "Hsien-chao"
+  orcid: "https://orcid.org/0000-0002-4870-9663"
+- family-names: "Kim"
+  given-names: "Sohyoung"
+- family-names: "Hu"
+  given-names: "Yue"
+- family-names: "Saloura"
+  given-names: "Vassiliki"
+title: "Cut And Run anaLysIS pipeLinE (CARLISLE)"
+version: 2.4.1
+url: "https://github.com/CCBR/CARLISLE"
\ No newline at end of file

From 463b23d6e906e4017a9d9b1c3ad5996df8fc649d Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Mon, 8 Jan 2024 18:01:17 -0500
Subject: [PATCH 21/26] docs: creating version docs

---
 VERSION | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 VERSION

diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..005119b
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+2.4.1

From 04c0a702f7d296215f83b234cdbe08340f82b2ee Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 11 Jan 2024 12:21:21 -0500
Subject: [PATCH 22/26] chore: add pre-commit & prettier config files

---
 .pre-commit-config.yaml | 48 +++++++++++++++++++++++++++++++++++++++++
 .prettierignore         |  8 +++++++
 .prettierrc             |  7 ++++++
 3 files changed, 63 insertions(+)
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 .prettierignore
 create mode 100644 .prettierrc

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..12dc373
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,48 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-json
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  # R formatting
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    hooks:
+      - id: style-files
+  # general linting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+  # enforce commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..f0a6037
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,8 @@
+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
diff --git a/.prettierrc b/.prettierrc
new file mode 100644
index 0000000..81ee40a
--- /dev/null
+++ b/.prettierrc
@@ -0,0 +1,7 @@
+overrides:
+  - files:
+      - "*.md"
+      - "*.cff"
+      - ".prettierrc"
+    options:
+      tabWidth: 2

From 4f451fabfaafea2594501a3772bdd5e2a19b51a0 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 11 Jan 2024 12:22:02 -0500
Subject: [PATCH 23/26] chore: update citation cff w/ zenodo DOI, affiliations,
 release date

---
 CITATION.cff | 40 ++++++++++++++++++++++++----------------
 1 file changed, 24 insertions(+), 16 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 9ea2218..b940de0 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,21 +1,29 @@
 cff-version: 1.2.0
 message: "If you use CARLISLE, please cite it as below."
 authors:
-- family-names: "Sevilla"
-  given-names: "Samantha"
-  orcid: "https://orcid.org/0000-0002-8734-9875"
-- family-names: "Koparde"
-  given-names: "Vishal"
-  orcid: "https://orcid.org/0000-0001-8978-8495"
-- family-names: "Chou"
-  given-names: "Hsien-chao"
-  orcid: "https://orcid.org/0000-0002-4870-9663"
-- family-names: "Kim"
-  given-names: "Sohyoung"
-- family-names: "Hu"
-  given-names: "Yue"
-- family-names: "Saloura"
-  given-names: "Vassiliki"
+  - family-names: "Sevilla"
+    given-names: "Samantha"
+    orcid: "https://orcid.org/0000-0002-8734-9875"
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: "Koparde"
+    given-names: "Vishal"
+    orcid: "https://orcid.org/0000-0001-8978-8495"
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: "Chou"
+    given-names: "Hsien-chao"
+    orcid: "https://orcid.org/0000-0002-4870-9663"
+  - family-names: "Kim"
+    given-names: "Sohyoung"
+  - family-names: "Hu"
+    given-names: "Yue"
+  - family-names: "Saloura"
+    given-names: "Vassiliki"
 title: "Cut And Run anaLysIS pipeLinE (CARLISLE)"
+url: https://ccbr.github.io/CARLISLE/
+repository-code: https://github.com/CCBR/CARLISLE
+identifiers:
+  - description: Archived snapshots of all versions
+    type: doi
+    value: 10.5281/zenodo.10483876
 version: 2.4.1
-url: "https://github.com/CCBR/CARLISLE"
\ No newline at end of file
+date-released: 2024-01-10

From 5c88b7c4aea464e36827bb9ff7924015471b98e2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 11 Jan 2024 12:25:02 -0500
Subject: [PATCH 24/26] docs: add DOI to readme

---
 README.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 70fea14..86643fd 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,11 @@
 
 <div align="center">
   <img src="resources/img/CUTandRUN_Workflow.jpeg" width="85%" height="85%">
-  
-  [![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)  [![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues) [![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)  
+
+[![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)  
+[![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues)
+[![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)  
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10483876.svg)](https://doi.org/10.5281/zenodo.10483876)
 
 </div>
 

From 72e6108eca64efdc5ae769892a8d9bb0e36f2a4b Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 11 Jan 2024 12:25:41 -0500
Subject: [PATCH 25/26] style: move badges outside center div

---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 86643fd..7baa755 100644
--- a/README.md
+++ b/README.md
@@ -2,14 +2,13 @@
 
 <div align="center">
   <img src="resources/img/CUTandRUN_Workflow.jpeg" width="85%" height="85%">
+</div>
 
 [![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)  
 [![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues)
 [![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)  
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10483876.svg)](https://doi.org/10.5281/zenodo.10483876)
 
-</div>
-
 This snakemake pipeline is built to run on [Biowulf](https://hpc.nih.gov/).
 
 For comments/suggestions/advice please reach out to [Samantha Chill](mailto:samantha.sevilla@nih.gov).

From 390d6c187391e28b3682f45741e99a1fae153ec7 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 11 Jan 2024 12:29:30 -0500
Subject: [PATCH 26/26] style: fix whitespace for badge center alignment

---
 README.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 7baa755..6b2a25c 100644
--- a/README.md
+++ b/README.md
@@ -2,13 +2,14 @@
 
 <div align="center">
   <img src="resources/img/CUTandRUN_Workflow.jpeg" width="85%" height="85%">
-</div>
 
-[![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)  
+[![GitHub releases](https://img.shields.io/github/release/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/releases)
 [![GitHub issues](https://img.shields.io/github/issues/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/issues)
-[![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)  
+[![GitHub license](https://img.shields.io/github/license/CCBR/CARLISLE)](https://github.com/CCBR/CARLISLE/blob/master/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10483876.svg)](https://doi.org/10.5281/zenodo.10483876)
 
+</div>
+
 This snakemake pipeline is built to run on [Biowulf](https://hpc.nih.gov/).
 
 For comments/suggestions/advice please reach out to [Samantha Chill](mailto:samantha.sevilla@nih.gov).