Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Changed paths of files used in main.nf.test from test-data/methylseq … #7212

Merged
merged 8 commits into from
Dec 13, 2024
Merged

Changed paths of files used in main.nf.test from test-data/methylseq … #7212

Changes from 2 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
61357c7
cnanged paths of files used in main.nf.test from test-data/methylseq …
Dec 13, 2024
dada39f
Merge branch 'master' into change_paths_parabricks/fq2bammeth/main.nf…
sateeshperi Dec 13, 2024
dbe487f
modified paths to include 'params.modules_testdata_base_path +'
Dec 13, 2024
46b31c9
Merge branch 'change_paths_parabricks/fq2bammeth/main.nf.test' of htt…
Dec 13, 2024
354b71c
Merge branch 'master' into change_paths_parabricks/fq2bammeth/main.nf…
sateeshperi Dec 13, 2024
5540880
removed extra ' in front of params
Dec 13, 2024
22401e3
Merge branch 'change_paths_parabricks/fq2bammeth/main.nf.test' of htt…
Dec 13, 2024
950c3b7
Merge branch 'nf-core:master' into change_paths_parabricks/fq2bammeth…
PanosProv Dec 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ nextflow_process {
"""
input[0] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
])
"""
}
Expand All @@ -34,12 +34,12 @@ nextflow_process {
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
]
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
])
input[2] = BWAMETH_INDEX.out.index
input[3] = []
Expand Down Expand Up @@ -68,12 +68,12 @@ nextflow_process {
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
]
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
])
input[2] = BWAMETH_INDEX.out.index
input[3] = []
Expand All @@ -98,13 +98,13 @@ nextflow_process {
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
]
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
file('https://github.com/nf-core/test-datasets/blob/modules/data/genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
])
input[2] = BWAMETH_INDEX.out.index
input[3] = []
Expand Down
Loading