Commit 4f3bee96 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

step 06

parent 5702351d
......@@ -17,15 +17,15 @@ workflow SHARED {
ch_prokka_reads = Channel.empty()
ch_prokka_faa = Channel.empty()
if ( ! params.skip_structural_annot ) {
PROKKA_AND_RENAME (ch_assembly)
ch_prokka_reads = PROKKA_AND_RENAME.out.gff.join(PROKKA_AND_RENAME.out.fna, remainder: true).join(ch_reads, remainder: true)
ch_prokka_faa = PROKKA_AND_RENAME.out.faa
STEP_04_STRUCTURAL_ANNOT (ch_assembly)
ch_prokka_reads = STEP_04_STRUCTURAL_ANNOT.out.gff.join(STEP_04_STRUCTURAL_ANNOT.out.fna, remainder: true).join(ch_reads, remainder: true)
ch_prokka_faa = STEP_04_STRUCTURAL_ANNOT.out.faa
}
if ( ! params.skip_alignment) {
STEP_05_ALIGNMENT(ch_prokka_reads, ch_prokka_faa)
}
if ( ! params.skip_func_annot) {
STEP_06_FUNC_ANNOT(PROKKA_AND_RENAME.out.fna)
STEP_06_FUNC_ANNOT(STEP_04_STRUCTURAL_ANNOT.out.fna)
}
emit:
......
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