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update workflow images and packed wf
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@KerstenBreuer
KerstenBreuer committed Oct 10, 2019
1 parent 75490fc commit 087ab18
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Binary file modified CWL/workflows/CUTnRUN_pipeline.cwl.pdf
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Binary file modified CWL/workflows/ChIPmentation_pipeline.cwl.pdf
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45 changes: 36 additions & 9 deletions CWL/workflows/ChIPmentation_pipeline.cwl_packed.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -1157,10 +1157,32 @@
"class": "CommandLineTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
"listing": [
{
"entryname": "tn5_overhang_correction.sh",
"entry": "BAM=\"$1\"\nOUTPUT_SUFFIX=\"$2\"\nIS_PAIRED_END=\"$3\"\nif [[ \"$IS_PAIRED_END\" == TRUE ]]\nthen\n samtools view -h -f 3 -F 16 \"$BAM\" | awk -f shifting_paired_end_plus_reads.awk > correcting.sam\n samtools view -f 19 \"$BAM\" | awk -f shifting_paired_end_minus_reads.awk >> correcting.sam\nelse\n samtools view -h -F 16 \"$BAM\" | awk -f shifting_single_end_plus_reads.awk > correcting.sam\n samtools view -f 16 \"$BAM\" | awk -f shifting_single_end_minus_reads.awk >> correcting.sam\nfi\nOUTFILE=\"\\${BAM##*/}\"\nOUTFILE=\"\\${OUTFILE%.bam}_\\${OUTPUT_SUFFIX}.bam\"\nsamtools sort -@ $(runtime.cores) -O bam -T sorting.bam -o \"$OUTFILE\" correcting.sam\n"
},
{
"entryname": "shifting_paired_end_plus_reads.awk",
"entry": "BEGIN {OFS=\"\\t\"}\n{\n if ( $1 ~ /^@/) { print }\n else if ($9>=38) {\n $4=$4+4; $8=$8-5; $9=$9-9; $11=\"*\";\n if ($8>0){ print } else {$8=1; print}\n }\n else if ($9<=-38) {\n $4=$4+4; $8=$8-5; $9=$9+9; $11=\"*\";\n if ($8>0){ print } else {$8=1; print}\n }\n}\n"
},
{
"entryname": "shifting_paired_end_minus_reads.awk",
"entry": "BEGIN {OFS=\"\\t\"}\n{\n if ($9>=38) {\n $4=$4-5; $8=$8+4; $9=$9-9; $11=\"*\"; \n if ($4>0){ print } else {$4=1; print}\n }\n else if ($9<=-38) {\n $4=$4-5; $8=$8+4; $9=$9+9; $11=\"*\"; \n if ($4>0){ print } else {$4=1; print}\n }\n}\n"
},
{
"entryname": "shifting_single_end_plus_reads.awk",
"entry": "BEGIN {OFS=\"\\t\"}\n{\n if ( $1 ~ /^@/) { print }\n else {\n $4=$4+4; $7=\"*\"; $8=0; $9=0; $11=\"*\"; print\n }\n}\n"
},
{
"entryname": "shifting_single_end_minus_reads.awk",
"entry": "BEGIN {OFS=\"\\t\"}\n{\n $4=$4-5; $7=\"*\"; $8=0; $9=0; $11=\"*\"; print\n}\n"
}
],
"class": "InitialWorkDirRequirement"
},
{
"class": "StepInputExpressionRequirement"
"class": "InlineJavascriptRequirement"
}
],
"hints": [
Expand All @@ -1176,33 +1198,38 @@
],
"baseCommand": [
"bash",
"-c"
],
"arguments": [
{
"valueFrom": "${\n var cmd_line = \"\";\n \n if ( inputs.is_paired_end ){ // for paired end data\n // unpaired will be removed\n \n ////// shift + strand reads\n cmd_line += \"samtools view -h -f 3 -F 16 \" + inputs.bam.path; // only properly paired reads with the\n // first read on the + strand are output;\n // the header is included\n \n cmd_line += \" | awk \\'BEGIN {OFS=\\\"\\\\t\\\"} \" +\n \"{ \" + \n \"if ( $1 ~ /^@/) { print }\" + //header lines are printed unmodified\n \"else if ($9>=38) { \" + \n \"$4=$4+4; $8=$8-5; $9=$9-9; $11=\\\"*\\\"; if ($8>0){ print } else {$8=1; print}}\" + // read start positions are shifted\n \"else if ($9<=-38) { \" + \n \"$4=$4+4; $8=$8-5; $9=$9+9; $11=\\\"*\\\"; if ($8>0){ print } else {$8=1; print}}\" + // read start positions are shifted\n \"}\\' > correcting.sam\";\n ///// shift - strand reads \n cmd_line += \" ; samtools view -f 19 \" + inputs.bam.path; // only properly paired reads with the\n // first read on the - strand are output;\n // the header is excluded\n \n cmd_line += \" | awk \\'BEGIN {OFS=\\\"\\\\t\\\"} \" +\n \"{ \" + \n \"if ($9>=38) { \" + \n \"$4=$4-5; $8=$8+4; $9=$9-9; $11=\\\"*\\\"; if ($4>0){ print } else {$4=1; print}}\" + // read start positions are shifted\n \"else if ($9<=-38) { \" + \n \"$4=$4-5; $8=$8+4; $9=$9+9; $11=\\\"*\\\"; if ($4>0){ print } else {$4=1; print}}\" + // read start positions are shifted\n \"}\\' >> correcting.sam\";\n \n \n }\n else { // for single end data\n \n ////// shift + strand reads\n cmd_line += \"samtools view -h -F 16 \" + inputs.bam.path; // paired end as well as\n // - strand reads are excluded\n // the header is included\n \n cmd_line += \" | awk \\'BEGIN {OFS=\\\"\\\\t\\\"} \" +\n \"{ \" + \n \"if ( $1 ~ /^@/ ) { print }\" + //header lines are printed unmodified\n \"else { $4=$4+4; $7=\\\"*\\\"; $8=0; $9=0; $11=\\\"*\\\"; print}\" + // read start positions are shifted\n \"}\\' > correcting.sam\";\n ///// shift - strand reads \n cmd_line += \" ; samtools view -f 16 \" + inputs.bam.path; // paired end as well as\n // + strand reads are excluded\n // the header is included\n \n cmd_line += \" | awk \\'BEGIN {OFS=\\\"\\\\t\\\"} \" +\n \"{ \" + \n \"$4=$4-5; $7=\\\"*\\\"; $8=0; $9=0; $11=\\\"*\\\"; print \" + // read start positions are shifted\n \"}\\' >> correcting.sam\";\n }\n \n cmd_line += \" ; samtools sort -@ \" + runtime.cores + \" -O bam -T sorting.bam -o \" + inputs.bam.nameroot + \"_\" + inputs.out_suffix + \".bam correcting.sam\";\n \n return cmd_line;\n}\n \n"
}
"tn5_overhang_correction.sh"
],
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#tn5_overhang_correction.cwl/bam"
},
{
"type": "boolean",
"inputBinding": {
"prefix": "TRUE",
"position": 3
},
"id": "#tn5_overhang_correction.cwl/is_paired_end"
},
{
"type": "string",
"default": "tn5correct",
"inputBinding": {
"position": 2
},
"id": "#tn5_overhang_correction.cwl/out_suffix"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.bam.nameroot + \"_\" + inputs.out_suffix + \".bam\")"
"glob": "$(\"*_\" + inputs.out_suffix + \".bam\")"
},
"id": "#tn5_overhang_correction.cwl/bam_tn5_corrected"
}
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Binary file modified CWL/workflows/ChIPseq_pipeline.cwl.pdf
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Binary file modified CWL/workflows/ChIPseq_pipeline_spike_in.cwl.pdf
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