Merge pull request #648 from maxplanck-ie/bugfix_noncoding_SE

Bugfix noncoding se

.ci_stuff/test_dag.sh

@@ -71,9 +71,9 @@ 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
+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
@@ -111,15 +111,15 @@ 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
+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 ] || [ $WC -ne 856 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 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
@@ -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 ] || [ $WC -ne 584 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 503 ]; then exit 1 ; fi
 

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.1.1
+  version: 2.1.2
 
 source:
   path: ../

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

snakePipes/__init__.py

@@ -1 +1 @@
-__version__ = '2.1.1'
+__version__ = '2.1.2'

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 or pipeline=="scrna-seq":
+    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:

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 or pipeline=="scrna-seq":
+        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:

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

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),