Add singularity cache to before script in ci

b53b14cf · Gervaise Henry · e10247c7 · b53b14cf
Commit b53b14cf authored 4 years ago by Gervaise Henry
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,6 +29,7 @@ build_badges:
    - tags
  before_script:
    - module load singularity/3.5.3
+    - export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/
    - chmod +x ./workflow/scripts/get_updated_badge_info.sh
  script:
    - echo "Building badges"
@@ -62,10 +63,10 @@ getBag:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-  - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli --version > version_deriva.txt
-  - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
-  - pytest -m getBag
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
+    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli --version > version_deriva.txt
+    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+    - pytest -m getBag
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -82,11 +83,11 @@ getData:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag --version > version_bdbag.txt
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxtest.zip
-  - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
-  - pytest -m getData
+    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag --version > version_bdbag.txt
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxtest.zip
+    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
+    - pytest -m getData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -103,19 +104,19 @@ parseMetadata:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
-  - rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
-  - exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
-  - study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
-  - endsRaw=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
-  - endsMeta="uk"
-  - endsManual="se"
-  - stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
-  - spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
-  - species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
-  - readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
-  - echo -e "${endsMeta},${endsRaw},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
-  - pytest -m parseMetadata
+    - singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
+    - rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
+    - exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
+    - study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
+    - endsRaw=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
+    - endsMeta="uk"
+    - endsManual="se"
+    - stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
+    - spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
+    - species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
+    - readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
+    - echo -e "${endsMeta},${endsRaw},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
+    - pytest -m parseMetadata
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -132,9 +133,9 @@ fastqc:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
-  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
-  - pytest -m fastqc
+    - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
+    - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+    - pytest -m fastqc
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -151,11 +152,11 @@ seqwho:
    - merge_requests
    - schedules
  script:
-  - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
-  - mkdir -p SeqWho_call_plots/test_data/fastq/small/
-  - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -h | grep -o Version.* > version_seqwho.txt
-  - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix
-  - pytest -m seqwho
+    - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
+    - mkdir -p SeqWho_call_plots/test_data/fastq/small/
+    - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -h | grep -o Version.* > version_seqwho.txt
+    - singularity run 'docker://gudmaprbk/seqwho0.0.1:1.0.0' seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix
+    - pytest -m seqwho
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -172,12 +173,12 @@ trimData:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
-  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
-  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
-  - readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
-  - readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
-  - pytest -m trimData
+    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
+    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
+    - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
+    - readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
+    - readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
+    - pytest -m trimData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -194,9 +195,9 @@ downsampleData:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
-  - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
-  - pytest -m downsampleData
+    - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
+    - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
+    - pytest -m downsampleData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -213,15 +214,15 @@ inferMetadata:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
-  - >
-    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
-    if [[ ${align} == "" ]]; then exit 1; fi
-  - >
-    singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
-    ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
-    if [[ ${ended} == "" ]]; then exit 1; fi
-  - pytest -m inferMetadata
+    - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
+    - >
+      align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
+      if [[ ${align} == "" ]]; then exit 1; fi
+    - >
+      singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
+      ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
+      if [[ ${ended} == "" ]]; then exit 1; fi
+    - pytest -m inferMetadata
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -238,17 +239,17 @@ alignData:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
-  - pytest -m alignData
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
+    - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
+    - pytest -m alignData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -266,16 +267,16 @@ dedupData:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
-  - >
-    for i in {"chr8","chr4","chrY"}; do
-      echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
-    done | singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' parallel -j 20 -k
-  - pytest -m dedupData
+    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
+    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
+    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
+    - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
+    - >
+      for i in {"chr8","chr4","chrY"}; do
+        echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
+      done | singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' parallel -j 20 -k
+    - pytest -m dedupData
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -293,15 +294,15 @@ countData:
    - merge_requests
    - schedules
  script:
-  - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/geneID.tsv
-  - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/Entrez.tsv
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/sequence/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se_countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
-  - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
-  - pytest -m makeFeatureCounts
+    - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/geneID.tsv
+    - ln -s /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/metadata/Entrez.tsv
+    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/sequence/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se_countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
+    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
+    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
+    - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
+    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
+    - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
+    - pytest -m makeFeatureCounts
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -319,9 +320,9 @@ makeBigWig:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
-  - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
-  - pytest -m makeBigWig
+    - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
+    - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
+    - pytest -m makeBigWig
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -337,12 +338,12 @@ dataQC:
  except:
    - merge_requests
  script:
-  - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
-  - >
-    for i in {"chr8","chr4","chrY"}; do
-      echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
-    done | singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
-  - pytest -m dataQC
+    - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
+    - >
+      for i in {"chr8","chr4","chrY"}; do
+        echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
+      done | singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
+    - pytest -m dataQC

 uploadInputBag:
  stage: unit
@@ -353,23 +354,23 @@ uploadInputBag:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-  - echo THIS IS A TEST FILE > test.txt
-  - >
-    md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
-    size=$(wc -c < ./test.txt) &&
-    exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) &&
-    if [ "${exist}" == "[]" ]; then
-      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
-      cookie=${cookie:11:-1} &&
-      loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
-      echo ${rid} test input bag created
-    else
-      rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
-      rid=${rid:8:-6} &&
-      echo ${rid} test input bag already exists
-    fi
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+    - echo THIS IS A TEST FILE > test.txt
+    - >
+      md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
+      size=$(wc -c < ./test.txt) &&
+      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) &&
+      if [ "${exist}" == "[]" ]; then
+        cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+        cookie=${cookie:11:-1} &&
+        loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
+        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
+        echo ${rid} test input bag created
+      else
+        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
+        rid=${rid:8:-6} &&
+        echo ${rid} test input bag already exists
+      fi

 uploadExecutionRun:
  stage: unit
@@ -380,20 +381,20 @@ uploadExecutionRun:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-  - >
-    exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
-    cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
-    cookie=${cookie:11:-1} &&
-    if [ "${exist}" == "[]" ]; then
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
-      echo ${rid} test execution run created
-    else
-      rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
-      rid=${rid:7:-6} &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
-      echo ${rid} test execution run already exists
-    fi
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+    - >
+      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
+      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+      cookie=${cookie:11:-1} &&
+      if [ "${exist}" == "[]" ]; then
+        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
+        echo ${rid} test execution run created
+      else
+        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
+        rid=${rid:7:-6} &&
+        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
+        echo ${rid} test execution run already exists
+      fi

 uploadQC:
  stage: unit
@@ -404,20 +405,20 @@ uploadQC:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-  - >
-    exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
-    cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
-    cookie=${cookie:11:-1} &&
-    if [ "${exist}" != "[]" ]; then
-      rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
-      for rid in ${rids}; do
-        singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
-      done
-      echo all old mRNA QC RIDs deleted
-    fi
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
-      echo ${rid} test mRNA QC created
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+    - >
+      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
+      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+      cookie=${cookie:11:-1} &&
+      if [ "${exist}" != "[]" ]; then
+        rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
+        for rid in ${rids}; do
+          singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
+        done
+        echo all old mRNA QC RIDs deleted
+      fi
+        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
+        echo ${rid} test mRNA QC created

 uploadProcessedFile:
  stage: unit
@@ -428,27 +429,27 @@ uploadProcessedFile:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-  - echo THIS IS A TEST FILE > 17-BTFJ_test.csv
-  - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
-  - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
-  - >
-    exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
-    cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
-    cookie=${cookie:11:-1} &&
-    if [ "${exist}" != "[]" ]; then
-      rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
-      for rid in ${rids}; do
-        singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
-      done
-      echo all old processed file RIDs deleted
-    fi
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+    - echo THIS IS A TEST FILE > 17-BTFJ_test.csv
+    - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
+    - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
+    - >
+      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
+      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+      cookie=${cookie:11:-1} &&
+      if [ "${exist}" != "[]" ]; then
+        rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
+        for rid in ${rids}; do
+          singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
+        done
+        echo all old processed file RIDs deleted
+      fi
      singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie:9} staging.gudmap.org ./deriva
      echo test processed file uploaded
-  - mkdir test
-  - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag test --archiver zip
-  - echo test output bag created
-  - pytest -m outputBag
+    - mkdir test
+    - singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' bdbag test --archiver zip
+    - echo test output bag created
+    - pytest -m outputBag

 uploadOutputBag:
  stage: unit
@@ -459,23 +460,23 @@ uploadOutputBag:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-  - echo THIS IS A TEST FILE > test.txt
-  - >
-    md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
-    size=$(wc -c < ./test.txt) &&
-    exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Output_Bag/File_MD5=${md5}) &&
-    if [ "${exist}" == "[]" ]; then
-      cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
-      cookie=${cookie:11:-1} &&
-      loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
-      rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BVDJ -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
-      echo ${rid} test output bag created
-    else
-      rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
-      rid=${rid:8:-6} &&
-      echo ${rid} test output bag already exists
-    fi
+    - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
+    - echo THIS IS A TEST FILE > test.txt
+    - >
+      md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
+      size=$(wc -c < ./test.txt) &&
+      exist=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Output_Bag/File_MD5=${md5}) &&
+      if [ "${exist}" == "[]" ]; then
+        cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
+        cookie=${cookie:11:-1} &&
+        loc=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
+        rid=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BVDJ -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+        echo ${rid} test output bag created
+      else
+        rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
+        rid=${rid:8:-6} &&
+        echo ${rid} test output bag already exists
+      fi


 generateVersions:
@@ -487,9 +488,9 @@ generateVersions:
    - merge_requests
    - schedules
  script:
-  - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
-  - python ./workflow/scripts/generate_versions.py -o software_versions
-  - python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
+    - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
+    - python ./workflow/scripts/generate_versions.py -o software_versions
+    - python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -508,8 +509,8 @@ human_BioHPC:
    - merge_requests
    - schedules
  script:
-  - mkdir -p hu
-  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2 ./hu/
+    - mkdir -p hu
+    - cp -R /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2 ./hu/

 mouse_BioHPC:
  stage: reference
@@ -520,8 +521,8 @@ mouse_BioHPC:
    - merge_requests
    - schedules
  script:
-  - mkdir -p mo
-  - cp -R /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2 ./mo/
+    - mkdir -p mo
+    - cp -R /project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/hisat2 ./mo/

 human_dev:
  stage: reference
@@ -532,22 +533,22 @@ human_dev:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=dev.gudmap.org
-  - refName=GRCh
-  - references=$(echo ${referenceBase}/${refName}${refHuVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=dev.gudmap.org
+    - refName=GRCh
+    - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

 mouse_dev:
  stage: reference
@@ -558,22 +559,22 @@ mouse_dev:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=dev.gudmap.org
-  - refName=GRCm
-  - references=$(echo ${referenceBase}/${refName}${refMoVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=dev.gudmap.org
+    - refName=GRCm
+    - references=$(echo ${referenceBase}/${refName}${refMoVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

 human_staging:
  stage: reference
@@ -584,22 +585,22 @@ human_staging:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=staging.gudmap.org
-  - refName=GRCh
-  - references=$(echo ${referenceBase}/${refName}${refHuVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=staging.gudmap.org
+    - refName=GRCh
+    - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

 mouse_staging:
  stage: reference
@@ -610,23 +611,23 @@ mouse_staging:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=staging.gudmap.org
-  - refName=GRCm
-  - refHuVersion=38.p6.vM22
-  - references=$(echo ${referenceBase}/${refName}${refMoVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=staging.gudmap.org
+    - refName=GRCm
+    - refHuVersion=38.p6.vM22
+    - references=$(echo ${referenceBase}/${refName}${refMoVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

 human_prod:
  stage: reference
@@ -637,22 +638,22 @@ human_prod:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=www.gudmap.org
-  - refName=GRCh
-  - references=$(echo ${referenceBase}/${refName}${refHuVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=www.gudmap.org
+    - refName=GRCh
+    - references=$(echo ${referenceBase}/${refName}${refHuVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi

 mouse_prod:
  stage: reference
@@ -663,23 +664,23 @@ mouse_prod:
    - merge_requests
    - schedules
  script:
-  - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - referenceBase=www.gudmap.org
-  - refName=GRCm
-  - refHuVersion=38.p6.vM22
-  - references=$(echo ${referenceBase}/${refName}${refMoVersion})
-  - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
-  - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
-  - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
-  - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
-  - curl --request GET ${query} > refQuery.json
-  - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
-  - loc=$(dirname ${refURL})
-  - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
-  - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
-  - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
-  - test=$(echo ${test} | grep -o ${filename})
-  - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
+    - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
+    - referenceBase=www.gudmap.org
+    - refName=GRCm
+    - refHuVersion=38.p6.vM22
+    - references=$(echo ${referenceBase}/${refName}${refMoVersion})
+    - GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
+    - GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
+    - GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
+    - query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE}/Used_Spike_Ins=false)
+    - curl --request GET ${query} > refQuery.json
+    - refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
+    - loc=$(dirname ${refURL})
+    - if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
+    - filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
+    - test=$(singularity run 'docker://gudmaprbk/deriva1.4:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
+    - test=$(echo ${test} | grep -o ${filename})
+    - if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi


 integration_se:
@@ -689,11 +690,11 @@ integration_se:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename SE_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
+    - pytest -m completionMultiqc --filename SE_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -714,11 +715,11 @@ integration_pe:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename PE_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
+    - pytest -m completionMultiqc --filename PE_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -741,9 +742,9 @@ failAmbiguousSpecies:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
  retry:
    max: 0
    when:
@@ -756,9 +757,9 @@ failTrunkation:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
  retry:
    max: 0
    when:
@@ -771,9 +772,9 @@ failMismatchR1R2:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
  retry:
    max: 0
    when:
@@ -786,9 +787,9 @@ failUnexpectedMeta:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
  retry:
    max: 0
    when:
@@ -801,9 +802,9 @@ failFileStructure:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
  retry:
    max: 0
    when:
@@ -816,9 +817,9 @@ failSeqType:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNDJ --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failSeqType_report.html
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNDJ --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failSeqType_report.html
  retry:
    max: 0
    when:
@@ -831,12 +832,12 @@ override_inputBag:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
-  - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./inputBagOverride_multiqc.html \;
-  - pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
+    - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./inputBagOverride_multiqc.html \;
+    - pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -856,12 +857,12 @@ override_fastq:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
-  - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./fastqOverride_multiqc.html \;
-  - pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6    --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
+    - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./fastqOverride_multiqc.html \;
+    - pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -881,12 +882,12 @@ override_species:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
-  - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
-  - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
+    - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
+    - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -906,12 +907,12 @@ override_stranded:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
-  - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./strandedOverride_multiqc.html \;
-  - pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
+    - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./strandedOverride_multiqc.html \;
+    - pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -931,12 +932,12 @@ override_spike:
    variables:
      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - hostname
-  - ulimit -a
-  - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
-  - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
-  - pytest -m completionMultiqc --filename spikeOverride_multiqc_data.json
+    - hostname
+    - ulimit -a
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
+    - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
+    - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
+    - pytest -m completionMultiqc --filename spikeOverride_multiqc_data.json
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
@@ -957,8 +958,8 @@ consistency:
    variables:
        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
  script:
-  - pytest -m consistencySE
-  - pytest -m consistencyPE
+    - pytest -m consistencySE
+    - pytest -m consistencyPE
  artifacts:
    name: "$CI_JOB_NAME"
    when: always