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

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merged 8 commits into from
Dec 13, 2024
+8 −8
Merged

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

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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
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16 changes: 8 additions & 8 deletions modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
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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(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + '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(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
])
input[2] = BWAMETH_INDEX.out.index
input[3] = []
Expand Down
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