synced chipseq workflows

chipseq_workflow/chipseq_utils.sh

@@ -127,6 +127,10 @@ export -f cs_lib_size
 ## create sorted genome file for dba counting
 cs_sync_order_chrominfo2bam(){
 
+if [ $# -ne 2 ]; then
+    echo "Usage: cs_sync_order_bam2bed <bam_file>  <chrom_info>" >&2 ; return;
+fi
+
 echo '
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
 
@@ -148,6 +152,11 @@ export -f cs_sync_order_chrominfo2bam
 
 
 cs_sync_order_bam2bed(){
+
+if [ $# -ne 2 ]; then
+    echo "Usage: cs_sync_order_bam2bed <bam_file>  <bed_file>" >&2 ; return;
+fi
+
 echo '
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
 

chipseq_workflow/cs_snippets.sh

@@ -133,7 +133,7 @@ ll $bamFiles
 
 ## convert the bams to sorted bed for fast counting
 for bamFile in $bamFiles; do
-    # DEBUG bamFile=/projects/bioinfo/holger/projects/khan_chipseq_h1/alignments_mmfilt/H1M_Dome_mmf.bam
+    # DEBUG bamFile=/projects/bioinfo/holger/projects/khan_chipsseq_h1/alignments_mmfilt/H1M_Dome_mmf.bam
     bamBaseName=$(basename $(basename $bamFile .bam) _mmf)
     mysub "${project}__ib__${bamBaseName}" " bamToBed -i $bamFile | sort -k1,1 -k2,2n  > ${bamBaseName}.sortedbam.bed" | joblist .bam2bed
 done