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Fix HEREDOC/versions.yml #71

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Fix HEREDOC/versions.yml #71

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6dd1d4c
Escaped newlines/tabs
WalshKieran Apr 17, 2023
21d9432
Fixed awk ver error (revert if container updated)
WalshKieran May 20, 2023
ddd0ccf
Fixed comma separated help text
WalshKieran Jun 29, 2023
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2 changes: 1 addition & 1 deletion modules/local/annotation/full_annotation/main.nf
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Expand Up @@ -40,8 +40,8 @@ process ANNOTATION {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' )
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
busybox: \$(busybox | head -1)
ucsc: $VERSION
END_VERSIONS
"""
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6 changes: 3 additions & 3 deletions modules/local/ciriquant/filter/main.nf
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Expand Up @@ -24,16 +24,16 @@ process CIRIQUANT_FILTER {
def VERSION = '1.3.4'
"""
grep -v "#" ${prefix}.gtf | awk '{print \$14}' | cut -d '.' -f1 > counts
grep -v "#" ${prefix}.gtf | awk -v OFS="\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp
grep -v "#" ${prefix}.gtf | awk -v OFS="\\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp
paste ${prefix}.tmp counts > ${prefix}_unfilt.bed

awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}_unfilt.bed > ${prefix}_filt.bed
grep -v '^\$' ${prefix}_filt.bed > ${prefix}_ciriquant

awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed
awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed
rm ${prefix}.gtf

awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed
awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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2 changes: 1 addition & 1 deletion modules/local/ciriquant/yml/main.nf
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Expand Up @@ -32,6 +32,6 @@ process CIRIQUANT_YML {
SAMTOOLS=`which samtools`

touch travis.yml
printf "name: ciriquant\ntools:\n bwa: \$BWA\n hisat2: \$HISAT2\n stringtie: \$STRINGTIE\n samtools: \$SAMTOOLS\n\nreference:\n fasta: ${fasta_path}\n gtf: ${gtf_path}\n bwa_index: ${bwa_path}/${bwa_prefix}\n hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml
printf "name: ciriquant\\ntools:\\n bwa: \$BWA\\n hisat2: \$HISAT2\\n stringtie: \$STRINGTIE\\n samtools: \$SAMTOOLS\\n\\nreference:\\n fasta: ${fasta_path}\\n gtf: ${gtf_path}\\n bwa_index: ${bwa_path}/${bwa_prefix}\\n hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml
"""
}
6 changes: 5 additions & 1 deletion modules/local/stringtie/prepde/main.nf
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Expand Up @@ -19,7 +19,11 @@ process STRINGTIE_PREPDE {

script:
"""
for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\n" >> samples.txt ; done
for file in \$(ls *.gtf); do
sample_id=\${file%".transcripts.gtf"}
touch samples.txt
printf "\$sample_id\\t\$file\\n" >> samples.txt
done

prepDE.py -i samples.txt

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