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RGI add parameter to save json files #252

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merged 7 commits into from Apr 14, 2023
Merged

RGI add parameter to save json files #252

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98a0815
Merge pull request #231 from nf-core/dev
jasmezz Feb 27, 2023
d354927
option to save json
Darcy220606 Mar 29, 2023
c51412b
update changelog and output.md
Darcy220606 Apr 13, 2023
1bca438
Update nextflow_schema.json
Darcy220606 Apr 13, 2023
6bed019
Merge branch 'dev' into rgi_json_save
Darcy220606 Apr 13, 2023
3b21dab
Merge branch 'nf-core:master' into rgi_json_save
Darcy220606 Apr 14, 2023
7d1b977
Add reviewer suggestions
Darcy220606 Apr 14, 2023
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9 changes: 8 additions & 1 deletion conf/modules.config
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Expand Up @@ -258,7 +258,14 @@ process {
path: { "${params.outdir}/arg/rgi/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*.{json,txt}"
pattern: "*.{txt}"
],
[
path: { "${params.outdir}/arg/rgi/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*.{json}",
enabled: params.arg_rgi_savejson
],
[
path: { "${params.outdir}/arg/rgi/${meta.id}/" },
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -96,6 +96,7 @@ params {
arg_fargene_orffinder = false

arg_skip_rgi = false
arg_rgi_savejson = false
arg_rgi_savetmpfiles = false
arg_rgi_alignmenttool = 'BLAST'
arg_rgi_includeloose = true
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10 changes: 8 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -250,7 +250,7 @@
"default": "Bacteria",
"fa_icon": "fab fa-accusoft",
"description": "Specify the kingdom that the input represents.",
"help_text": "Specifies the kingdom that the input sample is derived from and/or you wish to screen for\n\n> ⚠️ Prokka cannot annotate Eukaryotes.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--kingdom`",
"help_text": "Specifies the kingdom that the input sample is derived from and/or you wish to screen for\n\n> \u26a0\ufe0f Prokka cannot annotate Eukaryotes.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--kingdom`",
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"enum": ["Archaea", "Bacteria", "Mitochondria", "Viruses"]
},
"annotation_prokka_gcode": {
Expand Down Expand Up @@ -700,6 +700,12 @@
"description": "Skip RGI during the ARG-screening.",
"fa_icon": "fas fa-ban"
},
"arg_rgi_savejson": {
"type": "boolean",
"description": "Save RGI output .json file.",
"help_text": "When activated, this flag saves the `.json` file in the RGI output directory. The `.json` file contains the ARG predictions ina format that can be can be uploaded to the CARD Website for visualization. See [RGI documentation](https://github.com/arpcard/rgi) for more details . By default it is generated in the working directory but not saved because the files are quite large and are not required downstream in the pipeline. ",
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"fa_icon": "fas fa-ad"
},
"arg_rgi_savetmpfiles": {
"type": "boolean",
"fa_icon": "fas fa-save",
Expand Down Expand Up @@ -828,7 +834,7 @@
"default": 1000,
"description": "Minimum longest-contig length a sample must have to be screened with antiSMASH.",
"fa_icon": "fas fa-ruler-horizontal",
"help_text": "This specifies the minimum length that the longest contig must have for the entire sample to be screened by antiSMASH.\n\nAny samples that do not reach this length will be not be sent to antiSMASH, therefore you will not receive output for these samples in your `--outdir`.\n\n> ⚠️ This is not the same as `--bgc_antismash_contigminlength`, which specifies to only analyse contigs above that threshold but _within_ a sample that has already passed `--bgc_antismash_sampleminlength` sample filter!"
"help_text": "This specifies the minimum length that the longest contig must have for the entire sample to be screened by antiSMASH.\n\nAny samples that do not reach this length will be not be sent to antiSMASH, therefore you will not receive output for these samples in your `--outdir`.\n\n> \u26a0\ufe0f This is not the same as `--bgc_antismash_contigminlength`, which specifies to only analyse contigs above that threshold but _within_ a sample that has already passed `--bgc_antismash_sampleminlength` sample filter!"
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},
"bgc_antismash_contigminlength": {
"type": "integer",
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