Merge pull request #347 from vib-singlecell-nf/develop

Develop for 0.26.1

.github/ISSUE_TEMPLATE/bug_report.md

@@ -38,8 +38,8 @@ If applicable, add screenshots to help explain your problem.
 
 **Please complete the following information:**
  - OS: [e.g. Ubuntu]
- - Nextflow Version: [e.g. 20.04.1]
- - vsn-pipelines Version: [e.g. 0.14.2]
+ - Nextflow Version: [e.g. 20.10.0]
+ - vsn-pipelines Version: [e.g. 0.26.1]
 
 **Additional context**
 Add any other context about the problem here.

docs/getting-started.rst

@@ -23,7 +23,7 @@ Make sure you have the following software installed,
 
 - Nextflow_
 
-    - Currently VSN-Pipelines requires Nextflow version ``20.04.1``
+    - Currently VSN-Pipelines requires Nextflow version ``20.10.0`` or higher.
 
 - A container system, either of:
 
@@ -68,7 +68,7 @@ Example Output
 .. code:: shell
 
     $ nextflow -C nextflow.config run $VSN -entry single_sample
-    N E X T F L O W  ~  version 20.04.1
+    N E X T F L O W  ~  version 20.10.0
     Launching `/staging/leuven/stg_00002/lcb/dwmax/documents/aertslab/GitHub/vib-singlecell-nf/vsn-pipelines/main.nf` [silly_pare] - revision: 77be3ba59d
     WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
     executor >  local (83)

docs/pipelines.rst

@@ -559,7 +559,7 @@ First, generate the config :
 
 Make sure the following parts of the generated config are properly set:
 
-.. code:: bash
+.. code:: groovy
 
     [...]
     data {
@@ -597,9 +597,48 @@ Make sure the following parts of the generated config are properly set:
 
 Now we can run it with the following command:
 
-.. code:: groovy
+.. code:: bash
 
     nextflow -C nextflow.config \
        run ~/vib-singlecell-nf/vsn-pipelines \
        -entry cell_filter
 
+
+**sra** |sra|
+-------------
+
+.. |sra| image:: https://github.com/vib-singlecell-nf/vsn-pipelines/workflows/cell_annotate_filter/badge.svg
+
+Runs the ``sra`` workflow which will download all (or user-defined selected) FASTQ files from a particular SRA project ID and format with properly and humand friendly names.
+
+First, generate the config :
+
+.. code:: bash
+
+    nextflow config \
+      ~/vib-singlecell-nf/vsn-pipelines \
+      -profile sra,singularity \
+      > nextflow.config
+
+NOTE: If you're a VSC user, you might want to add the ``vsc`` profile.
+
+
+Now we can run it with the following command:
+
+.. code:: bash
+
+    nextflow -C nextflow.config \
+       run ~/vib-singlecell-nf/vsn-pipelines \
+       -entry cell_filter
+
+    $ nextflow -C nextflow.config run ~/vib-singlecell-nf/vsn-pipelines -entry sra
+    N E X T F L O W  ~  version 20.11.0-edge
+    Launching `~/vib-singlecell-nf/vsn-pipelines/main.nf` [cranky_kare] - revision: c5e34d476a
+    executor >  local (1)
+    [c3/4bf7a2] process > sra:DOWNLOAD_FROM_SRA:SRA_TO_METADATA (1)             [100%] 1 of 1 _
+    [-        ] process > sra:DOWNLOAD_FROM_SRA:DOWNLOAD_FASTQS_FROM_SRA_ACC_ID -
+    [-        ] process > sra:DOWNLOAD_FROM_SRA:NORMALIZE_SRA_FASTQS            -
+    [SRR11442507, scATAC_Control_Superior_and_Middle_Temporal_Gyri_1]
+    [SRR11442506, scATAC_Control_Substantia_Nigra_2]
+    ...
+

main.nf

@@ -1025,6 +1025,33 @@ workflow nemesh {
 
 }
 
+workflow sra {
+
+    main:
+        include {
+            getChannel as getSRAChannel;
+        } from './src/channels/sra' params(params)
+        include {
+            DOWNLOAD_FROM_SRA;
+        } from './src/utils/workflows/downloadFromSRA' params(params)
+        include {
+            PUBLISH;
+        } from "./src/utils/workflows/utils" params(params)
+
+        // Run 
+        DOWNLOAD_FROM_SRA( getSRAChannel( params.data.sra ) )
+        if(params.utils?.publish) {
+            PUBLISH(
+                DOWNLOAD_FROM_SRA.out,
+                null,
+                "fastqs",
+                null,
+                false
+            )
+        }  
+
+}
+
 workflow sra_cellranger_bbknn {
 
     main:

nextflow.config

@@ -3,7 +3,7 @@ manifest {
     name = 'vib-singlecell-nf/vsn-pipelines'
     description = 'A repository of pipelines for single-cell data in Nextflow DSL2'
     homePage = 'https://github.com/vib-singlecell-nf/vsn-pipelines'
-    version = '0.26.0'
+    version = '0.26.1'
     mainScript = 'main.nf'
     defaultBranch = 'master'
     nextflowVersion = '!>=20.10.0'

src/channels/sra.nf

@@ -7,13 +7,13 @@ workflow getChannel {
         sra
 
     main:
-        channel = Channel.fromList(
+        data_channel = Channel.fromList(
             sra
         ).map {
             it -> tuple(it.id, it.samples)
         }
 
     emit:
-        channel
+        data_channel
 
 }

src/utils/processes/utils.nf

@@ -434,15 +434,14 @@ process SC__PUBLISH {
 
     publishDir \
         "${getPublishDir(params.global.outdir,toolName)}", \
-        mode: "${params.utils.publish?.mode ? params.utils.publish.mode: 'link'}", \
-        saveAs: { filename -> "${outputFileName}" }
+        mode: "${params.utils.publish?.mode ? params.utils.publish.mode: 'link'}"
 
     label 'compute_resources__minimal'
 
     input:
         tuple \
             val(tag), \
-            path(f, stageAs: 'input_file'), \
+            path(f), \
             val(stashedParams)
         val(fileOutputSuffix)
         val(toolName)
@@ -464,9 +463,10 @@ process SC__PUBLISH {
             stashedParams
         )
         """
-        if [ ! -f ${outputFileName} ]; then
-            ln -s input_file "${outputFileName}"
-        fi
+        # In case f and outputFileName are colliding, rename to f to dummy tmp filename
+        mv ${f} tmp
+        # FIXME: should avoid copying data (currently it's the only option to work without causing #317 and #345)
+        cp -rL tmp "${outputFileName}"
         """
 }