Merge branch '42-update.params' into 'develop'

Resolve "Update params to current standards"

Closes #42

See merge request !61

.gitlab-ci.yml

@@ -138,7 +138,7 @@ detailed_3:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.0.1'
   - pytest -m count301
   artifacts:
     name: "$CI_JOB_NAME"
@@ -162,7 +162,7 @@ detailed_4:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion '3GEXv2' --version '2.1.1'
   - pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"

CHANGELOG.md

@@ -7,9 +7,10 @@
 **Background**
 * Add Nextflow Tower integration into CI (GHH's profile)
 * Add new layered config folders, including prepare for awsifying
-* Do not rely on astrocyte for final param settings
+* Update param to new standard
 
 *Known Bugs*
+* Vizapp does not yet work for Astrocyte
 * Running in CLI: to set --fastq path of file/s needs to be in quotes
 
 # v1.2.0

README.md

 |*master*|*develop*|
 |:-:|:-:|
-|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/master)|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/develop/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/develop)|
+|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/develop/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/develop)|
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2652622.svg)](https://doi.org/10.5281/zenodo.2652622)
 

workflow/main.nf

@@ -20,15 +20,14 @@ params.kitVersion = '3GEXv3'
 params.version = '3.1.0'
 params.astrocyte = false
 params.outDir = "${baseDir}/output"
-params.multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
-params.references = "${baseDir}/../docs/references.md"
 
+// Variable error test
 if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
   print("Cellranger Version 2.1.1 requires kitVersion 2")
   System.exit(32)	
 }
 
-// Assign variables if astrocyte
+// Define variables if astrocyte (or from config)
 if (params.astrocyte) {
   print("Running under astrocyte")
   params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
@@ -49,7 +48,7 @@ if (params.astrocyte) {
 }
 params.genomeLocationFull = params.genomeLocation+params.genome
 
-// Define regular variables
+// Define variables from input
 name = params.name
 designLocation = Channel
   .fromPath(params.designFile)
@@ -67,12 +66,15 @@ forceCells = params.forceCells
 chemistryParam = params.chemistryParam
 version = params.version
 outDir = params.outDir
-multiqcConf = params.multiqcConf
-references = params.references
 
+// Define constant variables
+multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
+references = "${baseDir}/../docs/references.md"
 
+/*
+ * checkDesignFile: check design file for errors
+ */
 process checkDesignFile {
-
   tag "${name}"
   module 'python/3.6.1-2-anaconda'
 
@@ -93,7 +95,6 @@ process checkDesignFile {
     fi
     python3 ${baseDir}/scripts/check_design.py -d \${noSpaceDesign} -f ${fastqList}
     """
-
 }
 
 
@@ -104,7 +105,6 @@ samples = designPaths
   .groupTuple()
   //.subscribe { println it }
 
-
 // Duplicate variables
 samples.into {
   samples211
@@ -130,9 +130,10 @@ chemistryParam301 = chemistryParam
 chemistryParam302 = chemistryParam
 chemistryParam310 = chemistryParam
 
-
+/*
+ * count211: run cellranger count version 2.1.1
+ */
 process count211 {
-
   queue '128GB,256GB,256GBv1,384GB'
   tag "${sample}"
   publishDir "${outDir}/${task.process}", mode: 'copy'
@@ -170,12 +171,12 @@ process count211 {
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }
-
 }
 
-
+/*
+ * count211: run cellranger count version 3.0.1
+ */
 process count301 {
-
   queue '128GB,256GB,256GBv1,384GB'
   tag "${sample}"
   publishDir "${outDir}/${task.process}", mode: 'copy'
@@ -214,12 +215,12 @@ process count301 {
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }
-
 }
 
-
+/*
+ * count211: run cellranger count version 3.0.2
+ */
 process count302 {
-
   queue '128GB,256GB,256GBv1,384GB'
   tag "${sample}"
   publishDir "${outDir}/${task.process}", mode: 'copy'
@@ -260,12 +261,12 @@ process count302 {
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }
-
 }
 
-
+/*
+ * count211: run cellranger count version 3.1.0
+ */
 process count310 {
-
   queue '128GB,256GB,256GBv1,384GB'
   tag "${sample}"
   publishDir "${outDir}/${task.process}", mode: 'copy'
@@ -305,12 +306,12 @@ process count310 {
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }
-
 }
 
-
+/*
+ * versions: collect too versions into a single yml
+ */
 process versions {
-
   tag "${name}"
   module 'python/3.6.1-2-anaconda:pandoc/2.7:multiqc/1.7'
 
@@ -329,15 +330,15 @@ process versions {
     python3 "${baseDir}/scripts/generate_versions.py" -f version_*.txt -o versions
     python3 "${baseDir}/scripts/generate_references.py" -r "${references}" -o references
     """
-
 }
 
-
+// Collect all metrics summaries reguardless of cellranger version
 metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302, metricsSummary310)
 
-
+/*
+ * multiqc: create multiqc report
+ */
 process multiqc {
-
   tag "${name}"
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
   module 'multiqc/1.7'
@@ -357,5 +358,4 @@ process multiqc {
     sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv
     multiqc -c ${multiqcConf} .
     """
-
 }