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Check modules and biobakerymgx pipeline #21

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merged 3 commits into from
Apr 25, 2024
Merged

Check modules and biobakerymgx pipeline #21

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340bd86
Updated outdir for kneaddata/kneaddata
LaurenGonsalves Apr 25, 2024
df6ebe3
Update snapshots
LaurenGonsalves Apr 25, 2024
3758edd
Updated pipeline
LaurenGonsalves Apr 25, 2024
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2 changes: 1 addition & 1 deletion modules/local/kneaddata/kneaddata/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ process KNEADDATA_KNEADDATA {
kneaddata \\
--input1 ${fastq_gz[0]} \\
--input2 ${fastq_gz[1]} \\
--output . \\
--output ./ \\
--output-prefix ${prefix}_kneaddata \\
--reference-db ${kneaddata_db} \\
--threads ${task.cpus} \\
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2 changes: 1 addition & 1 deletion modules/nf-core/metaphlan/mergemetaphlantables/nextflow.config
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50 changes: 45 additions & 5 deletions subworkflows/local/fastq_read_preprocessing_kneaddata/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,21 +3,61 @@
"content": [
{
"0": [

[
{
"id": "test2"
},
[
"test2_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
"test2_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
]
],
[
{
"id": "test"
},
[
"test_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
"test_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
]
]
],
"1": [

"all_samples_kneaddata_read_counts.tsv:md5,0cbc1c285d40c25876ce0675fe36f34b"
],
"2": [
"versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
"versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
"versions.yml:md5,bb0ae5552fe7c380606c211bcf91f2c8",
"versions.yml:md5,c97c9af1b0da5c6c85c297ad365653cc"
],
"preprocessed_fastq_gz": [

[
{
"id": "test2"
},
[
"test2_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
"test2_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
]
],
[
{
"id": "test"
},
[
"test_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
"test_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
]
]
],
"read_counts_tsv": [

"all_samples_kneaddata_read_counts.tsv:md5,0cbc1c285d40c25876ce0675fe36f34b"
],
"versions": [
"versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
"versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
"versions.yml:md5,bb0ae5552fe7c380606c211bcf91f2c8",
"versions.yml:md5,c97c9af1b0da5c6c85c297ad365653cc"
]
}
Expand All @@ -26,6 +66,6 @@
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-24T11:21:29.845724761"
"timestamp": "2024-04-25T21:47:34.07117763"
}
}
4 changes: 2 additions & 2 deletions subworkflows/local/fastq_read_taxonomy_metaphlan/main.nf
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Expand Up @@ -43,14 +43,14 @@ workflow FASTQ_READ_TAXONOMY_METAPHLAN {
ch_versions = ch_versions.mix(METAPHLAN_SGBTOGTDBPROFILE.out.versions)

// combine metaphlan profiles for merging
ch_gtdb_profiles_combined_tsv = ch_gtdb_profile_tsv
ch_metaphlan_profiles_combined_tsv = ch_metaphlan_profile_txt
.map { [ [ id:'all_samples' ], it[1] ] }
.groupTuple( sort: 'deep' )

//
// MODULE: Merge Metaphlan profiles
//
ch_metaphlan_profiles_merged_tsv = METAPHLAN_MERGEMETAPHLANTABLES ( ch_gtdb_profiles_combined_tsv ).txt
ch_metaphlan_profiles_merged_tsv = METAPHLAN_MERGEMETAPHLANTABLES ( ch_metaphlan_profiles_combined_tsv ).txt
ch_versions = ch_versions.mix(METAPHLAN_MERGEMETAPHLANTABLES.out.versions)

emit:
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2 changes: 1 addition & 1 deletion subworkflows/local/fastq_read_taxonomy_metaphlan/tests/main.nf.test.snap
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Expand Up @@ -28,6 +28,6 @@
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-24T10:29:04.201964325"
"timestamp": "2024-04-25T21:55:37.113549813"
}
}
4 changes: 2 additions & 2 deletions workflows/biobakerymgx/tests/main.nf.test.snap
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Expand Up @@ -28,13 +28,13 @@

],
[

"versions.yml:md5,d9f2edf37349457eccb7644ee1db2ae7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-24T22:51:47.767796873"
"timestamp": "2024-04-25T22:21:11.648598038"
}
}
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