From 4fe729d464d344292e2abdc7a8c69609c89d84b3 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 15:47:20 +0200 Subject: [PATCH 01/12] noncoding SE working --- snakePipes/shared/rules/FASTQ.snakefile | 17 +++++++++-------- snakePipes/shared/rules/umi_tools.snakefile | 17 +++++++++-------- snakePipes/workflows/mRNA-seq/Snakefile | 1 - .../workflows/noncoding-RNA-seq/Snakefile | 1 - 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/snakePipes/shared/rules/FASTQ.snakefile b/snakePipes/shared/rules/FASTQ.snakefile index 4088bb234..b6b738bcf 100644 --- a/snakePipes/shared/rules/FASTQ.snakefile +++ b/snakePipes/shared/rules/FASTQ.snakefile @@ -8,14 +8,15 @@ rule origFASTQ1: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) -rule origFASTQ2: - input: - indir+"/{sample}"+reads[1]+ext - output: - "originalFASTQ/{sample}"+reads[1]+".fastq.gz" - run: - if not os.path.exists(os.path.join(outdir,output[0])): - os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) +if pairedEnd: + rule origFASTQ2: + input: + indir+"/{sample}"+reads[1]+ext + output: + "originalFASTQ/{sample}"+reads[1]+".fastq.gz" + run: + if not os.path.exists(os.path.join(outdir,output[0])): + os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) if downsample: if pairedEnd: diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index c29710549..ad579641f 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -50,14 +50,15 @@ else: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) - rule FASTQ2: - input: - "originalFASTQ/downsample_{sample}"+reads[1]+".fastq.gz" if downsample else "originalFASTQ/{sample}"+reads[1]+".fastq.gz" - output: - "FASTQ/{sample}"+reads[1]+".fastq.gz" - run: - if not os.path.exists(os.path.join(outdir,output[0])): - os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) + if pairedEnd: + rule FASTQ2: + input: + "originalFASTQ/downsample_{sample}"+reads[1]+".fastq.gz" if downsample else "originalFASTQ/{sample}"+reads[1]+".fastq.gz" + output: + "FASTQ/{sample}"+reads[1]+".fastq.gz" + run: + if not os.path.exists(os.path.join(outdir,output[0])): + os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) #If DNA-mapping: if UMIDedup: diff --git a/snakePipes/workflows/mRNA-seq/Snakefile b/snakePipes/workflows/mRNA-seq/Snakefile index 2a81aaff1..9df3d3ebc 100755 --- a/snakePipes/workflows/mRNA-seq/Snakefile +++ b/snakePipes/workflows/mRNA-seq/Snakefile @@ -284,7 +284,6 @@ if not fromBAM: rule all: input: - # expand("FASTQ/{sample}{read}.fastq.gz", sample = samples, read = reads), run_FastQC(fastqc), run_Trimming(trim, fastqc), run_alignment_free(), # Salmon diff --git a/snakePipes/workflows/noncoding-RNA-seq/Snakefile b/snakePipes/workflows/noncoding-RNA-seq/Snakefile index 6595f20e3..79b64cae4 100755 --- a/snakePipes/workflows/noncoding-RNA-seq/Snakefile +++ b/snakePipes/workflows/noncoding-RNA-seq/Snakefile @@ -152,7 +152,6 @@ if not fromBAM: rule all: input: - expand("FASTQ/{sample}{read}.fastq.gz", sample = samples, read = reads), expand("TEcount/{sample}.cntTable", sample = samples), run_FastQC(fastqc), run_Trimming(trim, fastqc), From e340eb3fca00f17b134926092e9c52b33a583fdc Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 15:48:12 +0200 Subject: [PATCH 02/12] SE dag test --- .ci_stuff/test_dag.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index ec043855b..708d33047 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -133,6 +133,8 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1053 ]; then exit 1 ; fi # noncoding-RNA-seq WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 667 ]; then exit 1 ; fi +WC=`noncoding-RNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 667 ]; then exit 1 ; fi WC=`noncoding-RNA-seq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 503 ]; then exit 1 ; fi From 39d190bd5715b4e860485f3d5b6d7419de682d29 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 15:50:34 +0200 Subject: [PATCH 03/12] bump version --- conda-recipe/meta.yaml | 2 +- docs/content/News.rst | 5 +++++ snakePipes/__init__.py | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index a05ca5296..3d7f43685 100755 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: snakepipes - version: 2.1.1 + version: 2.1.2 source: path: ../ diff --git a/docs/content/News.rst b/docs/content/News.rst index 70ff3e076..f550397df 100755 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -1,5 +1,10 @@ snakePipes News =============== + +snakePipes 2.1.2 +---------------- +* small bug fix: SE mode in noncoding-RNA-seq pipeline + snakePipes 2.1.1 ---------------- * small bug fix: a typo in atac-seq pipeline diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py index 55fa725bd..f81156126 100755 --- a/snakePipes/__init__.py +++ b/snakePipes/__init__.py @@ -1 +1 @@ -__version__ = '2.1.1' +__version__ = '2.1.2' From 8575b0da39f04b6b6f1fe686b02ffa463d21ebc1 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:00:22 +0200 Subject: [PATCH 04/12] test dag --- .ci_stuff/test_dag.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 708d33047..26f9f2948 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -71,7 +71,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 831 ]; then exit 1 ; fi WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --DAG --trim --mapq 20 --UMIDedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 831 ]; then exit 1 ; fi WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 649 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 651 ]; then exit 1 ; fi WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 705 ]; then exit 1 ; fi #allelic From 3aee6fc170d94281329fe99fe88d260b25f4d273 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:13:19 +0200 Subject: [PATCH 05/12] dag --- .ci_stuff/test_dag.sh | 2 +- snakePipes/common_functions.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 26f9f2948..96668572e 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -73,7 +73,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 831 ]; then exit 1 ; fi WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 651 ]; then exit 1 ; fi WC=`DNA-mapping -i SE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --mapq 20 --dedup --properPairs | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 705 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 707 ]; then exit 1 ; fi #allelic WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1443 ]; then exit 1 ; fi diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py index bb5d07eec..09ebe3788 100644 --- a/snakePipes/common_functions.py +++ b/snakePipes/common_functions.py @@ -455,6 +455,7 @@ def commonYAMLandLogs(baseDir, workflowDir, defaults, args, callingScript): # save to configs.yaml in outdir config = defaults config.update(vars(args)) # This allows modifications of args after handling a user config file to still make it to the YAML given to snakemake! + #config.update({"pairedEnd": pairedEnd}) #this is evaluated at runtime write_configfile(os.path.join(args.outdir, '{}.config.yaml'.format(workflowName)), config) # merge cluster config files: 1) global one, 2) workflow specific one, 3) user provided one From 5a6248c5c77a89668dfa3a522d08a9673d8c69ee Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:20:49 +0200 Subject: [PATCH 06/12] dag --- .ci_stuff/test_dag.sh | 2 +- snakePipes/common_functions.py | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 96668572e..641ba9d5c 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -111,7 +111,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 852 ]; then exit 1 ; fi WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 902 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 741 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 742 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 526 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py index 09ebe3788..bb5d07eec 100644 --- a/snakePipes/common_functions.py +++ b/snakePipes/common_functions.py @@ -455,7 +455,6 @@ def commonYAMLandLogs(baseDir, workflowDir, defaults, args, callingScript): # save to configs.yaml in outdir config = defaults config.update(vars(args)) # This allows modifications of args after handling a user config file to still make it to the YAML given to snakemake! - #config.update({"pairedEnd": pairedEnd}) #this is evaluated at runtime write_configfile(os.path.join(args.outdir, '{}.config.yaml'.format(workflowName)), config) # merge cluster config files: 1) global one, 2) workflow specific one, 3) user provided one From b0e9d336a49ef355345f4a687fa56a616de34556 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:28:43 +0200 Subject: [PATCH 07/12] dag --- .ci_stuff/test_dag.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 641ba9d5c..21ef4567a 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -113,7 +113,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 902 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 742 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 526 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 527 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 797 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` From 322e8f5efd4bce23baa8aea5c028a827cac147b5 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:35:34 +0200 Subject: [PATCH 08/12] dag --- .ci_stuff/test_dag.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index 21ef4567a..df9cd46e2 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -115,11 +115,11 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 742 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 527 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 797 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 798 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 854 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 855 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 909 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 910 ]; then exit 1 ; fi WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 593 ]; then exit 1 ; fi #allelic From 9517ff6efdb54f3b578027dd808228bfa2d94544 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:46:01 +0200 Subject: [PATCH 09/12] dag --- .ci_stuff/test_dag.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index df9cd46e2..bf7803926 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -117,7 +117,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 527 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 798 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 855 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 856 ]; then exit 1 ; fi WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 910 ]; then exit 1 ; fi WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` From 19c2f358d647320643bfe7288645f24b6b544863 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 16:56:05 +0200 Subject: [PATCH 10/12] dag --- .ci_stuff/test_dag.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh index bf7803926..5d658ab4b 100755 --- a/.ci_stuff/test_dag.sh +++ b/.ci_stuff/test_dag.sh @@ -134,7 +134,7 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1053 ]; then exit 1 ; fi WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 667 ]; then exit 1 ; fi WC=`noncoding-RNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` -if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 667 ]; then exit 1 ; fi +if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 584 ]; then exit 1 ; fi WC=`noncoding-RNA-seq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l` if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 503 ]; then exit 1 ; fi From ecacc9b4d049b4f1ca3d02ad0d49fcb02ec2ce76 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 17:11:52 +0200 Subject: [PATCH 11/12] test --- snakePipes/shared/rules/FASTQ.snakefile | 2 +- snakePipes/shared/rules/umi_tools.snakefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/snakePipes/shared/rules/FASTQ.snakefile b/snakePipes/shared/rules/FASTQ.snakefile index b6b738bcf..389fa7a8c 100644 --- a/snakePipes/shared/rules/FASTQ.snakefile +++ b/snakePipes/shared/rules/FASTQ.snakefile @@ -8,7 +8,7 @@ rule origFASTQ1: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) -if pairedEnd: +if pairedEnd or pipeline=="scRNA-seq": rule origFASTQ2: input: indir+"/{sample}"+reads[1]+ext diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index ad579641f..897a502e8 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -50,7 +50,7 @@ else: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) - if pairedEnd: + if pairedEnd or pipeline=="scRNA-seq": rule FASTQ2: input: "originalFASTQ/downsample_{sample}"+reads[1]+".fastq.gz" if downsample else "originalFASTQ/{sample}"+reads[1]+".fastq.gz" From e2b90cb4ea04d16699c5f9bfeed37a85279f8290 Mon Sep 17 00:00:00 2001 From: katsikora Date: Tue, 16 Jun 2020 17:20:30 +0200 Subject: [PATCH 12/12] fix scRNAseq --- snakePipes/shared/rules/FASTQ.snakefile | 2 +- snakePipes/shared/rules/umi_tools.snakefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/snakePipes/shared/rules/FASTQ.snakefile b/snakePipes/shared/rules/FASTQ.snakefile index 389fa7a8c..6ca3b0f62 100644 --- a/snakePipes/shared/rules/FASTQ.snakefile +++ b/snakePipes/shared/rules/FASTQ.snakefile @@ -8,7 +8,7 @@ rule origFASTQ1: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) -if pairedEnd or pipeline=="scRNA-seq": +if pairedEnd or pipeline=="scrna-seq": rule origFASTQ2: input: indir+"/{sample}"+reads[1]+ext diff --git a/snakePipes/shared/rules/umi_tools.snakefile b/snakePipes/shared/rules/umi_tools.snakefile index 897a502e8..a773eb97f 100644 --- a/snakePipes/shared/rules/umi_tools.snakefile +++ b/snakePipes/shared/rules/umi_tools.snakefile @@ -50,7 +50,7 @@ else: if not os.path.exists(os.path.join(outdir,output[0])): os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) - if pairedEnd or pipeline=="scRNA-seq": + if pairedEnd or pipeline=="scrna-seq": rule FASTQ2: input: "originalFASTQ/downsample_{sample}"+reads[1]+".fastq.gz" if downsample else "originalFASTQ/{sample}"+reads[1]+".fastq.gz"