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Verified Commit 5911d120 authored by Laurent Modolo's avatar Laurent Modolo
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agat: add params to convertion processes

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src/nf_modules/agat/main.nf
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...@@ -19,7 +19,7 @@ process gff_to_bed { ...@@ -19,7 +19,7 @@ process gff_to_bed {
script: script:
""" """
zcat ${gff} > ${gff.baseName}.gff zcat ${gff} > ${gff.baseName}.gff
agat_convert_sp_gff2bed.pl --gff ${gff.baseName}.gff --sub cds -o ${gff.simpleName}.bed agat_convert_sp_gff2bed.pl ${params.gff_to_bed} --gff ${gff.baseName}.gff -o ${gff.simpleName}.bed
""" """
} }
...@@ -41,6 +41,6 @@ process gff_to_gtf { ...@@ -41,6 +41,6 @@ process gff_to_gtf {
script: script:
""" """
zcat ${gff} > ${gff.baseName}.gff zcat ${gff} > ${gff.baseName}.gff
agat_convert_sp_gff2gtf.pl --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf agat_convert_sp_gff2gtf.pl ${params.gff_to_gtf} --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf
""" """
} }
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