millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-26 01:09:55 +00:00
Code Issues Releases Packages Activity

Fix file header descriptions

Browse source
This commit is contained in:
James Fellows Yates 2022-03-25 15:21:52 +01:00
parent dfcf8f7b1a
commit b5f5c75504
2 changed files with 9 additions and 10 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

7
subworkflows/local/longread_preprocessing.nf
View file

@ -1,5 +1,8 @@
/*
Process long raw reads with porechop
*/
include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main' include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main' include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
workflow LONGREAD_PREPROCESSING { workflow LONGREAD_PREPROCESSING {
@ -23,7 +26,7 @@ workflow LONGREAD_PREPROCESSING {
FASTQC_POST ( PORECHOP.out.reads ) FASTQC_POST ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} ) ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
emit: emit:

10
subworkflows/local/shortread_fastp.nf
View file

@ -1,7 +1,6 @@
// /*
// Check input samplesheet and get read channels Process short raw reads with FastP
// */
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main' include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main' include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
@ -17,9 +16,6 @@ workflow SHORTREAD_FASTP {
// //
// STEP: Read clipping and merging // STEP: Read clipping and merging
// //
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
ch_input_for_fastp = reads ch_input_for_fastp = reads
.dump(tag: "pre-fastp_branch") .dump(tag: "pre-fastp_branch")
.branch{ .branch{