Fix nextflow/runner error, change singularity cache, and limit processes in unit ci to 20

.gitlab-ci.yml

@@ -46,44 +46,44 @@ getRef:
 trimData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5JA_1M.se -j `nproc` ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j `nproc` ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5JA_1M.se -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j 20 ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
   - pytest -m trimData
 
 alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bam.bai
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz --summary-file ${repRID}.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bam.bai
   - pytest -m alignData
 
 dedupData:
   stage: unit
   script:
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
-  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
   - for i in {"chr8","chr4","chrY"}; do 
-      echo "samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;";
-      done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j `nproc` -k
+      echo "samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;";
+      done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
   - pytest -m dedupData
   
 makeBigWig:
   stage: unit
   script:
-  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
+  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
   - pytest -m makeBigWig
 
 makeFeatureCounts:
   stage: unit
   script:
-  - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene_name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam 
+  - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T 20 -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene_name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam 
   - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
   - pytest -m makeFeatureCounts
 
@@ -97,20 +97,22 @@ inferMetadata:
   stage: unit
   script:
   - for i in {"chr8","chr4","chrY"}; do
-    echo " tin.py -i /project/BICF/BICF_Core/shared/gudmap/test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5JA_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j `nproc` -k > Q-Y5JA_1M.se.sorted.deduped.tin.xls
+    echo " tin.py -i /project/BICF/BICF_Core/shared/gudmap/test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5JA_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j 20 -k > Q-Y5JA_1M.se.sorted.deduped.tin.xls
   - pytest -m inferMetadata
 
 integration_se:
   stage: integration
   script:
-  - ulimit -u 16384
-  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
+  - hostname
+  - ulimit -a
+  - nextflow -bg run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
 
 integration_pe:
   stage: integration
   script:
-  - ulimit -u 16384
-  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png
+  - hostname
+  - ulimit -a
+  - nextflow -bg run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png
   artifacts:
     name: "$CI_JOB_NAME"
     when: always

workflow/conf/biohpc.config

@@ -37,7 +37,7 @@ process {
 
 singularity {
   enabled = true
-  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+  cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
 }
 
 env {