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Add beautiful md5sums

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This commit is contained in:
FriederikeHanssen 2021-02-23 14:57:07 +01:00
parent 5e365d5eff
commit 13733b2581
3 changed files with 58 additions and 10 deletions
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7
software/seqkit/split2/main.nf
View file

@ -50,7 +50,8 @@ process SEQKIT_SPLIT2 {
split2 \
$options.args \
--threads $task.cpus \
-1 $reads
-1 ${reads} \
--out-dir ${prefix}.split
echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
@ -61,7 +62,9 @@ process SEQKIT_SPLIT2 {
$options.args \
--threads $task.cpus \
-1 ${reads[0]} \
-2 ${reads[1]}
-2 ${reads[1]} \
--out-dir ${prefix}.split
echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
}

4
tests/software/seqkit/split2/main.nf
View file

@ -3,8 +3,8 @@
nextflow.enable.dsl = 2
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000' ] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2'] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 200' ] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 3'] )
workflow test_seqkit_split2_single_end_length {
def input = []

55
tests/software/seqkit/split2/test.yml
View file

@ -6,7 +6,11 @@
- seqkit_split2_single_end
- length
files:
- path: output/seqkit/
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: fb45cfec0d0d37f85abe81a0d299137e
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311
- name: seqkit split2 single-end size
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
@ -16,7 +20,12 @@
- seqkit_split2_single_end
- size
files:
- path: output/seqkit/
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: e76ac276819eb862c0a931755a220b50
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 79eb15ff1aac645308fab188915f9edf
- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
md5sum: f01fa62d34012a2e9cc48972dfe8c14c
- name: seqkit split2 single-end part
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
@ -26,7 +35,12 @@
- seqkit_split2_single_end
- part
files:
- path: output/seqkit/
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: c394bc973e1f0f9bda835e4a7610d2e1
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 152e4470b8caeed1fc1c0326f34aa4e6
- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d
- name: seqkit split2 paired-end length
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
@ -36,7 +50,14 @@
- seqkit_split2_paired_end
- length
files:
- path: output/seqkit/
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: fb45cfec0d0d37f85abe81a0d299137e
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311
- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
md5sum: 4e9704a4a0f4bcab4900b6fcd9323d8a
- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
md5sum: da93241d0cfa84d4b806e1e102c16977
- name: seqkit split2 paired-end size
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
@ -46,7 +67,18 @@
- seqkit_split2_paired_end
- size
files:
- path: output/seqkit/
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: e76ac276819eb862c0a931755a220b50
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 79eb15ff1aac645308fab188915f9edf
- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
md5sum: f01fa62d34012a2e9cc48972dfe8c14c
- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
md5sum: 357bfa5b981f34d87f682aebcf5e46fe
- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
md5sum: f48f3389d2870f4934139a901e5c4bb2
- path: output/seqkit/test.split/SRR396636_R2.part_003.fastq.gz
md5sum: d161aa05bac2f7d1823da0479949512b
- name: seqkit split2 paired-end part
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
@ -55,3 +87,16 @@
- seqkit_split2
- seqkit_split2_paired_end
- part
files:
- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
md5sum: c394bc973e1f0f9bda835e4a7610d2e1
- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
md5sum: 152e4470b8caeed1fc1c0326f34aa4e6
- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d
- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
md5sum: 228aff8f1e56050967476fcad164a4fc
- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
md5sum: 41047f3df10126c0df7f8e9bfd752b83
- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d