From 21217e5816ba06de7eea8cd333f83168ba1a84a7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 29 Dec 2020 01:09:57 -0600
Subject: [PATCH] Update unit test to use staging

---
 .gitlab-ci.yml | 62 +++++++++++++++++++++++++-------------------------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7b16c35..352305f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,7 +30,7 @@ getBag:
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
   - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli --version > version_deriva.txt
-  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F4
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
   - pytest -m getBag
   artifacts:
     name: "$CI_JOB_NAME"
@@ -49,8 +49,8 @@ getData:
   script:
   - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
-  - unzip ./test_data/bag/Q-Y5F4_inputBag.zip
-  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F4_inputBag Q-Y5F4 TEST
+  - unzip ./test_data/bag/Q-Y5F6_inputBag.zip
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
   - pytest -m getData
   artifacts:
     name: "$CI_JOB_NAME"
@@ -96,11 +96,11 @@ inferMetadata:
   script:
   - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
   - >
-    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F4_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
+    align=$(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/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5F4_1M.se.sorted.deduped.bam" 1>> Q-Y5F4_1M.se.inferMetadata.log &&
-    ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5F4_1M.se.inferMetadata.log` &&
+    singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/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/inferMeta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
     if [[ ${ended} == "" ]]; then exit 1; fi
   - pytest -m inferMetadata
   artifacts:
@@ -119,8 +119,8 @@ trimData:
     - merge_requests
   script:
   - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
-  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F4_1M.se ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz
-  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F4_1M.pe ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F4_1M.R2.fastq.gz
+  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
+  - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
   - readLengthSE=$(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
@@ -139,7 +139,7 @@ downsampleData:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F4_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
+  - 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
 
 alignData:
@@ -152,14 +152,14 @@ alignData:
   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-Y5F4_1M.se.unal.gz -S Q-Y5F4_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-Y5F4_1M.se_trimmed.fq.gz --summary-file Q-Y5F4_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-Y5F4_1M.se.bam Q-Y5F4_1M.se.sam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F4_1M.se.sorted.bam Q-Y5F4_1M.se.bam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F4_1M.se.sorted.bam Q-Y5F4_1M.se.sorted.bam.bai
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F4_1M.pe.unal.gz -S Q-Y5F4_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-Y5F4_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F4_1M.pe_val_2.fq.gz --summary-file Q-Y5F4_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-Y5F4_1M.pe.bam Q-Y5F4_1M.pe.sam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F4_1M.pe.sorted.bam Q-Y5F4_1M.pe.bam
-  - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F4_1M.pe.sorted.bam Q-Y5F4_1M.pe.sorted.bam.bai
+  - 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/GRCh38.p12.v31/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/GRCh38.p12.v31/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"
@@ -179,12 +179,12 @@ dedupData:
   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-Y5F4_1M.se.sorted.bam O=Q-Y5F4_1M.se.deduped.bam M=Q-Y5F4_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-Y5F4_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F4_1M.se.deduped.bam
-  - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F4_1M.se.sorted.deduped.bam Q-Y5F4_1M.se.sorted.deduped.bam.bai
+  - 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-Y5F4_1M.se.sorted.deduped.bam ${i} > Q-Y5F4_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F4_1M.se.sorted.deduped.${i}.bam Q-Y5F4_1M.se.sorted.deduped.${i}.bam.bai;";
+      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:
@@ -205,9 +205,9 @@ countData:
   script:
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F4_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F4_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-Y5F4_1M.se.countData
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F4_1M.se
+  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/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
@@ -229,7 +229,7 @@ makeBigWig:
     - merge_requests
   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-Y5F4_1M.se.sorted.deduped.bam -o Q-Y5F4_1M.se.bw
+  - 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: "$CI_JOB_NAME"
@@ -247,7 +247,7 @@ fastqc:
     - merge_requests
   script:
   - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
-  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz -o .
+  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
   - pytest -m fastqc
   artifacts:
     name: "$CI_JOB_NAME"
@@ -265,11 +265,11 @@ dataQC:
   except:
     - merge_requests
   script:
-  - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F4_1M.se.sorted.deduped.tin.xls
+  - 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-Y5F4_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F4_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
-    done | singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F4_1M.se.sorted.deduped.tin.xls
+      echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/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:
@@ -655,7 +655,7 @@ override_inputBag:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F4 --inputBagForce ./test_data/bag/Q-Y5F4_inputBag_20201228.zip --upload false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_20201228.zip --upload false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
@@ -677,7 +677,7 @@ override_fastq:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F4 --fastqsForce './test_data/fastq/small/Q-Y5F4_1M.R{1,2}.fastq.gz' --upload false --ci true
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --ci true
   - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
   artifacts:
     name: "$CI_JOB_NAME"
-- 
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