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Modified tree structure #332

Merged
merged 9 commits into from
Feb 11, 2025
Merged

Modified tree structure #332

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e3e62c0
new tree structure
Feb 6, 2025
394caab
created yml file for local modules
Feb 7, 2025
73c4a88
create meta.yml
Feb 7, 2025
e193ec7
new yml files
Feb 7, 2025
1f667bb
local subworkflows yml
Feb 7, 2025
75fb1e0
fix yml
Feb 7, 2025
bab0756
update all modules
Feb 7, 2025
f654791
prettier
Feb 7, 2025
72826b0
linting
Feb 7, 2025
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36 changes: 18 additions & 18 deletions modules.json
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Expand Up @@ -7,62 +7,62 @@
"nf-core": {
"bbmap/align": {
"branch": "master",
"git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"bbmap/bbduk": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"bbmap/bbnorm": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"bbmap/index": {
"branch": "master",
"git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"hmmer/hmmsearch": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"pigz/compress": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"prodigal": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"prokka": {
"branch": "master",
"git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"samtools/flagstat": {
Expand Down Expand Up @@ -92,33 +92,33 @@
},
"seqtk/mergepe": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"seqtk/seq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"spades": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "9508616bf800acc767de4678d6b86cfcb27b9aeb",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"taxonkit/lineage": {
"branch": "master",
"git_sha": "90c5156bfa6326edadbeff4a1ca196c6d10fd2ec",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"],
"patch": "modules/nf-core/taxonkit/lineage/taxonkit-lineage.diff"
},
"trimgalore": {
"branch": "master",
"git_sha": "8d3e71002c5008e3f68a691ad8cd32c346356258",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
}
}
Expand Down
49 changes: 0 additions & 49 deletions modules/local/cat/cat_contigs.nf
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33 changes: 0 additions & 33 deletions modules/local/cat/cat_db.nf
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36 changes: 0 additions & 36 deletions modules/local/cat/cat_db_generate.nf
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29 changes: 0 additions & 29 deletions modules/local/cat/cat_summary.nf
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7 changes: 7 additions & 0 deletions modules/local/collect/featurecounts/environment.yml
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@@ -0,0 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
2 changes: 1 addition & 1 deletion modules/local/collect_featurecounts.nf → modules/local/collect/featurecounts/main.nf
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Expand Up @@ -2,7 +2,7 @@ process COLLECT_FEATURECOUNTS {
tag "$meta.id"
label 'process_high'

conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"
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31 changes: 31 additions & 0 deletions modules/local/collect/featurecounts/meta.yml
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@@ -0,0 +1,31 @@
name: "collect_featurecounts"
description: Collects and processes featureCounts output files
keywords:
- featurecounts
- collect
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- inputfiles:
type: file
description: Input featureCounts TSV files
pattern: "*.featureCounts.tsv"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- counts:
type: file
description: Processed counts TSV file
pattern: "*.counts.tsv.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@danilodileo"
7 changes: 7 additions & 0 deletions modules/local/collect/stats/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
2 changes: 1 addition & 1 deletion modules/local/collect_stats.nf → modules/local/collect/stats/main.nf
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Expand Up @@ -2,7 +2,7 @@ process COLLECT_STATS {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"
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45 changes: 45 additions & 0 deletions modules/local/collect/stats/meta.yml
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name: "collect_stats"
description: Collects and processes various statistics from different analysis steps
keywords:
- stats
- collect
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- samples:
type: value
description: List of sample names
- trimlogs:
type: file
description: Trimming log files
pattern: "*.trimming_report.txt"
- bblogs:
type: file
description: BBDuk log files
pattern: "*.bbduk.log"
- idxstats:
type: file
description: SAMtools idxstats output files
pattern: "*.idxstats"
- fcs:
type: file
description: Feature counts output file
pattern: "*.featureCounts.tsv"
- mergetab:
type: file
description: Merged taxonomy and function statistics file (optional)
pattern: "*.tsv"
output:
- overall_stats:
type: file
description: Compiled overall statistics file
pattern: "*.overall_stats.tsv.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@danilodileo"
7 changes: 7 additions & 0 deletions modules/local/diamond/blastp/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "diamond:2.1.10"
0 modules/local/diamond/blastp.nf → modules/local/diamond/blastp/main.nf
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