Merge pull request #684 from maxplanck-ie/minor_fixes_KS

Minor fixes ks

.ci_stuff/test_dag.sh

@@ -22,7 +22,7 @@ touch SE_input/sample1_R1.fastq.gz \
       SE_input/sample5_R1.fastq.gz \
       SE_input/sample6_R1.fastq.gz
 # Needed by ChIP and ATAC workflows
-mkdir -p BAM_input/deepTools_qc/bamPEFragmentSize BAM_input/filtered_bam BAM_input/Sambamba
+mkdir -p BAM_input/deepTools_qc/bamPEFragmentSize BAM_input/filtered_bam BAM_input/Sambamba BAM_input/bamCoverage 
 touch BAM_input/sample1.bam \
       BAM_input/sample2.bam \
       BAM_input/sample3.bam \
@@ -47,8 +47,15 @@ touch BAM_input/sample1.bam \
       BAM_input/Sambamba/sample4.markdup.txt \
       BAM_input/Sambamba/sample5.markdup.txt \
       BAM_input/Sambamba/sample6.markdup.txt \
-      BAM_input/deepTools_qc/bamPEFragmentSize/fragmentSize.metric.tsv
-mkdir -p allelic_BAM_input/allelic_bams allelic_BAM_input/filtered_bam  allelic_BAM_input/deepTools_qc/bamPEFragmentSize allelic_BAM_input/Sambamba
+      BAM_input/deepTools_qc/bamPEFragmentSize/fragmentSize.metric.tsv \
+      BAM_input/bamCoverage/sample1.filtered.seq_depth_norm.bw \
+      BAM_input/bamCoverage/sample2.filtered.seq_depth_norm.bw \
+      BAM_input/bamCoverage/sample3.filtered.seq_depth_norm.bw \
+      BAM_input/bamCoverage/sample4.filtered.seq_depth_norm.bw \
+      BAM_input/bamCoverage/sample5.filtered.seq_depth_norm.bw \
+      BAM_input/bamCoverage/sample6.filtered.seq_depth_norm.bw 
+
+mkdir -p allelic_BAM_input/allelic_bams allelic_BAM_input/filtered_bam  allelic_BAM_input/deepTools_qc/bamPEFragmentSize allelic_BAM_input/Sambamba allelic_BAM_input/bamCoverage/allele_specific
 touch allelic_BAM_input/allelic_bams/sample1.genome1.sorted.bam \
       allelic_BAM_input/allelic_bams/sample1.genome2.sorted.bam \
       allelic_BAM_input/allelic_bams/sample2.genome1.sorted.bam \
@@ -91,7 +98,13 @@ touch allelic_BAM_input/allelic_bams/sample1.genome1.sorted.bam \
       allelic_BAM_input/Sambamba/sample3.markdup.txt \
       allelic_BAM_input/Sambamba/sample4.markdup.txt \
       allelic_BAM_input/Sambamba/sample5.markdup.txt \
-      allelic_BAM_input/Sambamba/sample6.markdup.txt
+      allelic_BAM_input/Sambamba/sample6.markdup.txt \
+      allelic_BAM_input/bamCoverage/allele_specific/sample1.genome1.seq_depth_norm.bw \
+      allelic_BAM_input/bamCoverage/allele_specific/sample2.genome1.seq_depth_norm.bw \
+      allelic_BAM_input/bamCoverage/allele_specific/sample3.genome1.seq_depth_norm.bw \
+      allelic_BAM_input/bamCoverage/allele_specific/sample4.genome1.seq_depth_norm.bw \
+      allelic_BAM_input/bamCoverage/allele_specific/sample5.genome1.seq_depth_norm.bw \
+      allelic_BAM_input/bamCoverage/allele_specific/sample6.genome1.seq_depth_norm.bw 
 mkdir -p output
 touch /tmp/genes.gtf /tmp/genome.fa /tmp/genome.fa.fai /tmp/rmsk.txt /tmp/genes.bed /tmp/spikein_genes.gtf
 mkdir -p allelic_input
@@ -143,16 +156,19 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1443 ]; then exit 1 ; fi
 
 # ChIP-seq
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 439 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 401 ]; then exit 1 ; fi
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 441 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 403 ]; then exit 1 ; fi
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --singleEnd .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 439 ]; then exit 1 ; fi
-WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 401 ]; then exit 1 ; fi
+WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --bigWigType log2ratio .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 363 ]; then exit 1 ; fi
 # fromBAM
 WC=`ChIP-seq -d outdir --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 715 ]; then exit 1 ; fi
+# spikein
+WC=`ChIP-seq -d BAM_input --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp"  .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 433 ]; then exit 1 ; fi
 # fromBAM and spikein
 WC=`ChIP-seq -d outdir --useSpikeInForNorm --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/spikein_organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 591 ]; then exit 1 ; fi
@@ -232,13 +248,13 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 310 ]; then exit 1 ; fi
 
 # ATAC-seq
 WC=`ATAC-seq -d BAM_input --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 454 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 416 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller Genrich .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 520 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 482 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --peakCaller HMMRATAC .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 512 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 474 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --maxFragmentSize 120 --qval 0.1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 454 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 416 ]; then exit 1 ; fi
 WC=`ATAC-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM BAM_input/filtered_bam/ .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 686 ]; then exit 1 ; fi
 

conda-recipe/meta.yaml

@@ -11,9 +11,9 @@ build:
 
 requirements:
   host:
-    - python >=3
+    - python ==3.7
   run:
-    - python >=3.7
+    - python ==3.7
     - snakemake ==5.18.0
     - pandas
     - graphviz

docs/content/News.rst

@@ -1,6 +1,15 @@
 snakePipes News
 ===============
 
+snakePipes 2.2.2
+----------------
+
+* Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d.
+* DESeq2 Rmd file is not deleted anymore in noncoding-RNAseq.
+* Python version is fixed at 3.7.
+* Fixed labels in deepTools commands.
+* Allele_info is now boolean.
+
 snakePipes 2.2.1
 ----------------
 

snakePipes/__init__.py

@@ -1 +1 @@
-__version__ = '2.2.1'
+__version__ = '2.2.2'

snakePipes/shared/rscripts/CSAW.R

@@ -10,7 +10,7 @@ pairedEnd <- as.logical(snakemake@params[["pairedEnd"]])
 fraglength <- as.numeric(snakemake@params[["fragmentLength"]])  # used when the data is not paired end
 windowSize <- as.numeric(snakemake@params[["windowSize"]])
 importfunc <- snakemake@params[["importfunc"]]  #"DB_functions.R"
-allelic_info <- as.logical(snakemake@params[["allele_info"]])
+allelic_info <- as.logical(toupper(snakemake@params[["allele_info"]]))
 outdir<-snakemake@params[["outdir"]]
 yaml_path<-snakemake@params[["yaml_path"]]
 useSpikeInForNorm<-snakemake@params[["useSpikeInForNorm"]]

snakePipes/shared/rscripts/noncoding-DESeq2.R

@@ -139,5 +139,4 @@ sessionInfo()
 sink()
 
 ## ~~~~~~ 9. clean up ~~~~~
-file.remove('DESeq2_report_basic.Rmd')
 file.remove('citations.bib')