diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4a11c4f68110bbc81818780cedbf3b02c86cd3b4..7b16c353a47c48457c978c1f1cad3c7edec3832e 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=16-DNBG
+ - 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
- pytest -m getBag
artifacts:
name: "$CI_JOB_NAME"
@@ -49,8 +49,8 @@ getData:
script:
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- - unzip ./test_data/bag/16-DNBG_inputBag.zip
- - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh 16-DNBG_inputBag 16-DNBG TEST
+ - unzip ./test_data/bag/Q-Y5F4_inputBag.zip
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F4_inputBag Q-Y5F4 TEST
- pytest -m getData
artifacts:
name: "$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 $(grep "Overall alignment rate" ./test_data/meta/16-DNBG_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
+ align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F4_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/16-DNBG_1M.se.sorted.deduped.bam" 1>> 16-DNBG_1M.se.inferMetadata.log &&
- ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/inferMeta.sh endness 16-DNBG_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-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` &&
if [[ ${ended} == "" ]]; then exit 1; fi
- pytest -m inferMetadata
artifacts:
@@ -119,8 +119,8 @@ trimData:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
- - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename 16-DNBG_1M.se ./test_data/fastq/small/16-DNBG_1M.R1.fastq.gz
- - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename 16-DNBG_1M.pe ./test_data/fastq/small/16-DNBG_1M.R1.fastq.gz ./test_data/fastq/small/16-DNBG_1M.R2.fastq.gz
+ - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F4_1M.se ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz
+ - singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F4_1M.pe ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F4_1M.R2.fastq.gz
- readLengthSE=$(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/16-DNBG_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-Y5F4_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 16-DNBG_1M.se.unal.gz -S 16-DNBG_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/16-DNBG_1M.se_trimmed.fq.gz --summary-file 16-DNBG_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 16-DNBG_1M.se.bam 16-DNBG_1M.se.sam
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-DNBG_1M.se.sorted.bam 16-DNBG_1M.se.bam
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-DNBG_1M.se.sorted.bam 16-DNBG_1M.se.sorted.bam.bai
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz 16-DNBG_1M.pe.unal.gz -S 16-DNBG_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/16-DNBG_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/16-DNBG_1M.pe_val_2.fq.gz --summary-file 16-DNBG_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 16-DNBG_1M.pe.bam 16-DNBG_1M.pe.sam
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-DNBG_1M.pe.sorted.bam 16-DNBG_1M.pe.bam
- - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-DNBG_1M.pe.sorted.bam 16-DNBG_1M.pe.sorted.bam.bai
+ - 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
- 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/16-DNBG_1M.se.sorted.bam O=16-DNBG_1M.se.deduped.bam M=16-DNBG_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
- - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools sort -@ 20 -O BAM -o 16-DNBG_1M.se.sorted.deduped.bam ./test_data/bam/small/16-DNBG_1M.se.deduped.bam
- - singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/16-DNBG_1M.se.sorted.deduped.bam 16-DNBG_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-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
- >
for i in {"chr8","chr4","chrY"}; do
- echo "samtools view -b 16-DNBG_1M.se.sorted.deduped.bam ${i} > 16-DNBG_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b 16-DNBG_1M.se.sorted.deduped.${i}.bam 16-DNBG_1M.se.sorted.deduped.${i}.bam.bai;";
+ 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;";
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 16-DNBG_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/16-DNBG_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/16-DNBG_1M.se.countData
- - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID 16-DNBG_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-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
- 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/16-DNBG_1M.se.sorted.deduped.bam -o 16-DNBG_1M.se.bw
+ - 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
- pytest -m makeBigWig
artifacts:
name: "$CI_JOB_NAME"
@@ -247,7 +247,7 @@ fastqc:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
- - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/16-DNBG_1M.R1.fastq.gz -o .
+ - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F4_1M.R1.fastq.gz -o .
- pytest -m fastqc
artifacts:
name: "$CI_JOB_NAME"
@@ -265,11 +265,11 @@ dataQC:
except:
- merge_requests
script:
- - echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > 16-DNBG_1M.se.sorted.deduped.tin.xls
+ - echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F4_1M.se.sorted.deduped.tin.xls
- >
for i in {"chr8","chr4","chrY"}; do
- echo "tin.py -i ./test_data/bam/small/16-DNBG_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat 16-DNBG_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"
- done | singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> 16-DNBG_1M.se.sorted.deduped.tin.xls
+ echo "tin.py -i ./test_data/bam/small/Q-Y5F4_1M.se.sorted.deduped.${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
- 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 16-DNBG --inputBagForce ./test_data/bag/16-DNBG_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-Y5F4 --inputBagForce ./test_data/bag/Q-Y5F4_inputBag_20201228.zip --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -677,7 +677,7 @@ override_fastq:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNBG --fastqsForce './test_data/fastq/small/16-DNBG_1M.R{1,2}.fastq.gz' --upload false --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F4 --fastqsForce './test_data/fastq/small/Q-Y5F4_1M.R{1,2}.fastq.gz' --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py
index cd0de436082182aeb1eb2ca3c84762dcd09cc9b1..11f0f3d0d09236a3f3494a2c851fb4294f2a1323 100644
--- a/workflow/tests/test_alignReads.py
+++ b/workflow/tests/test_alignReads.py
@@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.alignData
def test_alignData_se():
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.unal.gz'))
+ data_output_path, 'Q-Y5F6_1M.se.unal.gz'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.bam'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai'))
@pytest.mark.alignData
def test_alignData_pe():
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.pe.unal.gz'))
+ data_output_path, 'Q-Y5F6_1M.pe.unal.gz'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.pe.sorted.bam'))
+ data_output_path, 'Q-Y5F6_1M.pe.sorted.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.pe.sorted.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai'))
diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py
index f36541a7ec12c39f2196044571bb342a248bc1c5..55df66deaeda6dac18ea26455dd1e3948ceb28ba 100644
--- a/workflow/tests/test_dataQC.py
+++ b/workflow/tests/test_dataQC.py
@@ -12,9 +12,9 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.dataQC
def test_dataQC():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.se.sorted.deduped.tin.xls'))
+ test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.tin.xls'))
assert countLines(os.path.join(test_output_path,
- '16-DNBG_1M.se.sorted.deduped.tin.xls'))
+ 'Q-Y5F6_1M.se.sorted.deduped.tin.xls'))
def countLines(fileName):
diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py
index 082359ae25417208c181288f4c8e81f00dddcb6f..89fc2b10fa4db847ccc16d5cce664bf551b29ee3 100644
--- a/workflow/tests/test_dedupReads.py
+++ b/workflow/tests/test_dedupReads.py
@@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.dedupData
def test_dedupData():
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.bam'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chr8.bam'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chr8.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chr4.bam'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chr4.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam.bai'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chrY.bam'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.sorted.deduped.chrY.bam.bai'))
+ data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai'))
diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py
index b3238727e58e0673d81ae45e6a3ef9eaf3ae630f..07e76108fbfc92f945060d8e5d1e1ea8f74e6a4a 100644
--- a/workflow/tests/test_fastqc.py
+++ b/workflow/tests/test_fastqc.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.fastqc
def test_fastqc():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.R1_fastqc.zip'))
+ test_output_path, 'Q-Y5F6_1M.R1_fastqc.zip'))
diff --git a/workflow/tests/test_getBag.py b/workflow/tests/test_getBag.py
index 55d08d950ff4ac078c9d1c9756787545321c7346..23bfc0ea50c260a2f5c4cbf62321c066b5743ac2 100644
--- a/workflow/tests/test_getBag.py
+++ b/workflow/tests/test_getBag.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getBag
def test_getBag():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_inputBag.zip'))
+ test_output_path, 'Q-Y5F6_inputBag.zip'))
diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py
index 2b08dfbcf53f4e05d72988d78cd812981e898a63..596a120abe904eac8f3e0ad871c9f8c03a6cba5f 100644
--- a/workflow/tests/test_getData.py
+++ b/workflow/tests/test_getData.py
@@ -12,6 +12,6 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.getData
def test_getData():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_inputBag/bagit.txt'))
+ test_output_path, 'Q-Y5F6_inputBag/bagit.txt'))
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_inputBag/data/assets/Study/16-DMQG/Experiment/16-DMW0Replicate/16-DNBG/22967_gene_counts.txt'))
+ test_output_path, 'Q-Y5F6_inputBag/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/Q-Y5F6/mMARIS_Six2-#3.gene.rpkm.txt'))
diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py
index c9d918e29cb574aa40bfabf0197caa2e23073343..7485163631e2604ac2d5477a5c27b2fc9b235b44 100644
--- a/workflow/tests/test_inferMetadata.py
+++ b/workflow/tests/test_inferMetadata.py
@@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.inferMetadata
def test_inferMetadata():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.se.inferMetadata.log'))
+ test_output_path, 'Q-Y5F6_1M.se.inferMetadata.log'))
diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py
index 5793befa818d5b5ca991f81c778aeb62c94f6937..d8f62f5edfb3b57868d0b4b18ed6a0deb6bd651e 100644
--- a/workflow/tests/test_makeBigWig.py
+++ b/workflow/tests/test_makeBigWig.py
@@ -11,4 +11,4 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.makeBigWig
def test_makeBigWig():
- assert os.path.exists(os.path.join(data_output_path, '16-DNBG_1M.se.bw'))
+ assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.bw'))
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index 08af331703aecd53f61a37f65cd1566d43e22527..f6373b99109e1d618dcb65559d24977140a125a4 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -12,8 +12,8 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.makeFeatureCounts
def test_makeFeatureCounts():
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.countData'))
+ data_output_path, 'Q-Y5F6_1M.se.countData'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se.countTable.csv'))
+ data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
assert os.path.exists(os.path.join(
- data_output_path, '16-DNBG_1M.se_tpmTable.csv'))
+ data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
index 528fe52458cb8a98d5ec022693c53e84ddf72e3c..a0938e756715fb30254e5c72fee4cd38bffec330 100644
--- a/workflow/tests/test_trimData.py
+++ b/workflow/tests/test_trimData.py
@@ -12,12 +12,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.trimData
def test_trimData_se():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.se_trimmed.fq.gz'))
+ test_output_path, 'Q-Y5F6_1M.se_trimmed.fq.gz'))
@pytest.mark.trimData
def test_trimData_pe():
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.pe_val_1.fq.gz'))
+ test_output_path, 'Q-Y5F6_1M.pe_val_1.fq.gz'))
assert os.path.exists(os.path.join(
- test_output_path, '16-DNBG_1M.pe_val_2.fq.gz'))
+ test_output_path, 'Q-Y5F6_1M.pe_val_2.fq.gz'))