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Merge pull request #19 from N-Hoffmann/stringtie
Add stringtie2 support
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,35 @@ | ||
| #!/bin/bash | ||
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| # Format a gtf file with only 12 fields if more (to be used by overlap) | ||
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| #!/bin/bash | ||
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| # Format a bed file to an tabulated bed | ||
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| # USAGE | ||
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| usage() { | ||
| echo "#" >&2 | ||
| echo "# Format a gtf 12+ in cleaned gtf 12 to be used by overlap...">&2 | ||
| echo "# USAGE: `basename $0` <file.gtf>">&2 | ||
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| } | ||
| ################################################################################ | ||
| infile=$1 | ||
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| if [ -p /dev/stdin ];then | ||
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| #from STDIN | ||
| cat /dev/stdin | awk '{for (i=1;i<9;i++) {printf("%s\t",$i) }; for (i=9;i<=NF;i++) {printf("%s ",$i)}; print ""}' | ||
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| elif [ $# -eq 1 ];then | ||
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| awk '{for (i=1;i<9;i++) {printf("%s\t",$i) }; for (i=9;i<=NF;i++) {printf("%s ",$i)}; print ""}' $infile | ||
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| else | ||
| echo "#Error! no argument file or file empty !" | ||
| usage; | ||
| exit 0; | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| process GFFCOMPARE { | ||
| conda (params.enable_conda ? "bioconda::gffcompare" : null) | ||
| container "${ workflow.containerEngine == 'singularity' ? | ||
| 'https://depot.galaxyproject.org/singularity/gffcompare:0.12.6--h9f5acd7_0' : | ||
| 'biocontainers/gffcompare:0.12.6--h9f5acd7_0' }" | ||
| publishDir "$params.outdir/stringtie2", mode: 'copy', pattern: 'extended_annotations.gtf' | ||
| cpus params.maxCpu | ||
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| input: | ||
| input: | ||
| path reference_gtf | ||
| path fasta | ||
| path merged_gtf | ||
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| output: | ||
| path("*.annotated.gtf"), emit: annotated_gtf | ||
| path("*.loci") , emit: loci | ||
| path("*.stats") , emit: stats | ||
| path("*.tracking") , emit: tracking | ||
| path("extended_annotations.gtf"), emit: stringtie_gtf | ||
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| shell: | ||
| ''' | ||
| gffcompare \ | ||
| -r !{reference_gtf} \ | ||
| -s !{fasta} \ | ||
| !{merged_gtf} | ||
| #Reformat the output of gffcompare to correctly match novel isoforms to known genes | ||
| awk 'BEGIN{ | ||
| while(getline<"gffcmp.tracking">0){ | ||
| if ($4 !="u" && $4 !="r"){ | ||
| split($3,gn,"|"); | ||
| split($5,tx,"|"); | ||
| final["\\""tx[2]"\\";"]="\\""gn[1]"\\";" | ||
| } | ||
| } | ||
| } { | ||
| if ($12 in final){ | ||
| $10=final[$12]; print $0} else {print $0} | ||
| }' !{merged_gtf} | gtf2gtf_cleanall.sh > extended_annotations.gtf | ||
| ''' | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| process MERGE_COUNTS { | ||
| publishDir "$params.outdir/stringtie2", mode: 'copy', pattern: '*.txt' | ||
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| input: | ||
| path gene_counts | ||
| path tx_counts | ||
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| output: | ||
| path "counts_gene.txt", emit: gene_counts | ||
| path "counts_transcript.txt", emit: tx_counts | ||
| path "empty.ndr", emit: ndr | ||
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| shell: | ||
| ''' | ||
| # Merge the individual outputs of featurecount of each .bam into a single file | ||
| paste !{gene_counts} \ | ||
| | awk '{printf("%s ",$1); for (i=2;i<=NF;i+=2){printf("%s ",$i)}print "\\n"}' \ | ||
| | grep -v -e "^$" \ | ||
| | awk -v OFS='\\t' '{$1=$1}1' > counts_gene.txt | ||
| paste !{tx_counts} \ | ||
| | awk '{printf("\\n%s %s ",$1,$2); for (i=3;i<=NF;i+=3){printf("%s ",$i)}}' \ | ||
| | grep -v -e "^$" \ | ||
| | awk -v OFS='\\t' '{$1=$1}1' > counts_transcript.txt | ||
| # Create empty NDR file for TFKMERS to have same workflow as bambu in filtering step | ||
| # (placeholder, not used) | ||
| touch empty.ndr | ||
| ''' | ||
| } |
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