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Proposal: Rename output from fastp module (#1802)

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* Rename output from fastp module

* UPdate tests

* fix alignment

* prettier

* Update modules/fastp/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* apply review suggestion -sf

* typo

* update md5

* update md5

* try with human data

* revert, human data also doesn't work

* use contains instead

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
This commit is contained in:
FriederikeHanssen 2022-06-24 10:01:14 +02:00 committed by GitHub
parent 1363130410
commit 9b51362a53
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3 changed files with 34 additions and 34 deletions
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14
modules/fastp/main.nf
View file

@ -13,7 +13,7 @@ process FASTP {
val save_merged val save_merged
output: output:
tuple val(meta), path('*.trim.fastq.gz') , optional:true, emit: reads tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.json') , emit: json
tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.html') , emit: html
tuple val(meta), path('*.log') , emit: log tuple val(meta), path('*.log') , emit: log
@ -31,10 +31,10 @@ process FASTP {
if (meta.single_end) { if (meta.single_end) {
def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
""" """
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz [ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
fastp \\ fastp \\
--in1 ${prefix}.fastq.gz \\ --in1 ${prefix}.fastq.gz \\
--out1 ${prefix}.trim.fastq.gz \\ --out1 ${prefix}.fastp.fastq.gz \\
--thread $task.cpus \\ --thread $task.cpus \\
--json ${prefix}.fastp.json \\ --json ${prefix}.fastp.json \\
--html ${prefix}.fastp.html \\ --html ${prefix}.fastp.html \\
@ -50,13 +50,13 @@ process FASTP {
def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : '' def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
""" """
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
fastp \\ fastp \\
--in1 ${prefix}_1.fastq.gz \\ --in1 ${prefix}_1.fastq.gz \\
--in2 ${prefix}_2.fastq.gz \\ --in2 ${prefix}_2.fastq.gz \\
--out1 ${prefix}_1.trim.fastq.gz \\ --out1 ${prefix}_1.fastp.fastq.gz \\
--out2 ${prefix}_2.trim.fastq.gz \\ --out2 ${prefix}_2.fastp.fastq.gz \\
--json ${prefix}.fastp.json \\ --json ${prefix}.fastp.json \\
--html ${prefix}.fastp.html \\ --html ${prefix}.fastp.html \\
$fail_fastq \\ $fail_fastq \\

2
modules/fastp/meta.yml
View file

@ -38,7 +38,7 @@ output:
- reads: - reads:
type: file type: file
description: The trimmed/modified/unmerged fastq reads description: The trimmed/modified/unmerged fastq reads
pattern: "*trim.fastq.gz" pattern: "*fastp.fastq.gz"
- json: - json:
type: file type: file
description: Results in JSON format description: Results in JSON format

42
tests/modules/fastp/test.yml
View file

@ -3,18 +3,18 @@
tags: tags:
- fastp - fastp
files: files:
- path: output/fastp/test.fastp.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.html - path: output/fastp/test.fastp.html
contains: contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)" - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "single end (151 cycles)" - "single end (151 cycles)"
- path: output/fastp/test.fastp.json
md5sum: 7ee735cefb67f549dc857eefb9e7f123
- path: output/fastp/test.fastp.log - path: output/fastp/test.fastp.log
contains: contains:
- "Q20 bases: 12922(92.9841%)" - "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99" - "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.json
md5sum: a517ba37b17a342b5428f2c1f8fe3dd7
- name: fastp test_fastp_paired_end - name: fastp test_fastp_paired_end
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -25,16 +25,16 @@
contains: contains:
- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)" - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
- "The input has little adapter percentage (~0.000000%), probably it's trimmed before." - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
- path: output/fastp/test.fastp.json
contains:
- '"passed_filter_reads": 198'
- path: output/fastp/test.fastp.log - path: output/fastp/test.fastp.log
contains: contains:
- "No adapter detected for read1" - "No adapter detected for read1"
- "Q30 bases: 12281(88.3716%)" - "Q30 bases: 12281(88.3716%)"
- path: output/fastp/test.fastp.json - path: output/fastp/test_1.fastp.fastq.gz
contains:
- '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4 md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test_2.trim.fastq.gz - path: output/fastp/test_2.fastp.fastq.gz
md5sum: 532b190fb4dc7b2277ee5cf1464e598c md5sum: 532b190fb4dc7b2277ee5cf1464e598c
- name: fastp test_fastp_single_end_trim_fail - name: fastp test_fastp_single_end_trim_fail
@ -42,20 +42,20 @@
tags: tags:
- fastp - fastp
files: files:
- path: output/fastp/test.fail.fastq.gz
md5sum: b57f2026eb259a0b0c0b3960c270258d
- path: output/fastp/test.fastp.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.html - path: output/fastp/test.fastp.html
contains: contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)" - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "single end (151 cycles)" - "single end (151 cycles)"
- path: output/fastp/test.fastp.json
md5sum: feafc4181a2a61b4b52d9c2b59b419ad
- path: output/fastp/test.fastp.log - path: output/fastp/test.fastp.log
contains: contains:
- "Q20 bases: 12922(92.9841%)" - "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99" - "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.json
md5sum: 4be682c727942a45fc4c8600c28694a8
- path: output/fastp/test.fail.fastq.gz
md5sum: b57f2026eb259a0b0c0b3960c270258d
- name: fastp test_fastp_paired_end_trim_fail - name: fastp test_fastp_paired_end_trim_fail
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -73,14 +73,14 @@
- path: output/fastp/test.fastp.json - path: output/fastp/test.fastp.json
contains: contains:
- '"passed_filter_reads": 198' - '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test_2.trim.fastq.gz
md5sum: 532b190fb4dc7b2277ee5cf1464e598c
- path: output/fastp/test_1.fail.fastq.gz - path: output/fastp/test_1.fail.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/fastp/test_1.fastp.fastq.gz
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test_2.fail.fastq.gz - path: output/fastp/test_2.fail.fastq.gz
md5sum: 72d0002841967676ac936d08746a9128 md5sum: 72d0002841967676ac936d08746a9128
- path: output/fastp/test_2.fastp.fastq.gz
md5sum: 532b190fb4dc7b2277ee5cf1464e598c
- name: fastp test_fastp_paired_end_merged - name: fastp test_fastp_paired_end_merged
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -102,7 +102,7 @@
- "total bases: 13683" - "total bases: 13683"
- path: output/fastp/test.merged.fastq.gz - path: output/fastp/test.merged.fastq.gz
md5sum: 4955ca2c899729b17bd526d2626a8d73 md5sum: 4955ca2c899729b17bd526d2626a8d73
- path: output/fastp/test_1.trim.fastq.gz - path: output/fastp/test_1.fastp.fastq.gz
md5sum: 4a03721ee252b7c6e81e007550e6ab63 md5sum: 4a03721ee252b7c6e81e007550e6ab63
- path: output/fastp/test_2.trim.fastq.gz - path: output/fastp/test_2.fastp.fastq.gz
md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace