Bump fastp (nf-core#3419)

* bump fastp * test.yml * remove empty checksum * update fastq_fastqc_umitools_fastp
EgorGuga · May 15, 2023 · 37a98dd · 37a98dd
1 parent 0342d85
commit 37a98dd
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Showing 3 changed files with 17 additions and 15 deletions.
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
@@ -2,10 +2,10 @@ process FASTP {
  tag "$meta.id"
  label 'process_medium'
 
- conda "bioconda::fastp=0.23.2"
+ conda "bioconda::fastp=0.23.3"
  container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
- 'biocontainers/fastp:0.23.2--h79da9fb_0' }"
+ 'https://depot.galaxyproject.org/singularity/fastp:0.23.3--h5f740d0_0' :
+ 'biocontainers/fastp:0.23.3--h5f740d0_0' }"
 
  input:
  tuple val(meta), path(reads)

diff --git a/tests/modules/nf-core/fastp/test.yml b/tests/modules/nf-core/fastp/test.yml
@@ -1,5 +1,5 @@
 - name: fastp test_fastp_single_end
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:
@@ -16,14 +16,14 @@
  - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
  - "single end (151 cycles)"
  - path: output/fastp/test.fastp.json
- md5sum: 7ee735cefb67f549dc857eefb9e7f123
+ md5sum: 7924d53fb5bb4a589d52d6ff5d4d46ad
  - path: output/fastp/test.fastp.log
  contains:
  - "Q20 bases: 12922(92.9841%)"
  - "reads passed filter: 99"
 
 - name: fastp test_fastp_paired_end
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:
@@ -56,7 +56,7 @@
  - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
 
 - name: fastp test_fastp_interleaved
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:
@@ -73,14 +73,14 @@
  - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
  - "paired end (151 cycles + 151 cycles)"
  - path: output/fastp/test.fastp.json
- md5sum: 25ec85e3534f380ca2109c894671f1ed
+ md5sum: 1dae6048670eef91c9b85f7de544300c
  - path: output/fastp/test.fastp.log
  contains:
  - "Q20 bases: 12922(92.9841%)"
  - "reads passed filter: 198"
 
 - name: fastp test_fastp_single_end_trim_fail
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:
@@ -102,14 +102,14 @@
  - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
  - "single end (151 cycles)"
  - path: output/fastp/test.fastp.json
- md5sum: feafc4181a2a61b4b52d9c2b59b419ad
+ md5sum: 696ad8d22d9fa6d960dc8d0285985321
  - path: output/fastp/test.fastp.log
  contains:
  - "Q20 bases: 12922(92.9841%)"
  - "reads passed filter: 99"
 
 - name: fastp test_fastp_paired_end_trim_fail
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:
@@ -141,14 +141,16 @@
  - "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
  - "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
  - path: output/fastp/test_1.fail.fastq.gz
+ - path: output/fastp/test_1.fastp.fastq.gz
+ md5sum: dc08e42319d0deab088da4d8600aa2bd
  - path: output/fastp/test_2.fail.fastq.gz
  contains:
  - "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/2"
  - "CTTAGGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAA"
  - "A//AA6EEAEEEEE6EEE/EEA/EA///AAE/EAEEEAE6AE/E/E/EEAAE/EAA/E/E/<EA//E/6"
 
 - name: fastp test_fastp_paired_end_merged
- command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/fastp/nextflow.config
+ command: nextflow run ./tests/modules/nf-core/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastp/nextflow.config
  tags:
  - fastp
  files:

diff --git a/tests/subworkflows/nf-core/fastq_fastqc_umitools_fastp/test.yml b/tests/subworkflows/nf-core/fastq_fastqc_umitools_fastp/test.yml
@@ -12,16 +12,16 @@
  contains:
  - "fastp report"
  - path: output/fastp/test.fastp.json
- md5sum: cfc3e8b871b9bc770f1dc16432d64e67
+ md5sum: 938c90235ea690480007805fda2e8abb
  - path: output/fastp/test.fastp.log
  contains:
  - "No adapter detected for read1"
  - "No adapter detected for read2"
  - "Read1 before filtering:"
  - path: output/fastp/test_1.fastp.fastq.gz
- md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
+ md5sum: dc08e42319d0deab088da4d8600aa2bd
  - path: output/fastp/test_2.fastp.fastq.gz
- md5sum: 532b190fb4dc7b2277ee5cf1464e598c
+ md5sum: e59d0d65cc8c2801f1b970df601fc207
  - path: output/fastqc/test_1_fastqc.html
  contains: ["test_1.gz FastQC Report"]
  - path: output/fastqc/test_2_fastqc.html