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Update docs + some fix #329

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merged 7 commits into from
Jan 20, 2021
Merged

Update docs + some fix #329

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2b62a1a
fix: update docs to close #327
maxulysse Jan 20, 2021
532f7e3
fix: escape $ sign cf @szilvajuhos @jfnavarro
maxulysse Jan 20, 2021
aa99711
add: Update list of collaborators @jfnavarro
maxulysse Jan 20, 2021
5214fd0
fix: remove unnecessary modification to input file for Control-FREEC
maxulysse Jan 20, 2021
47af921
fix: correct input for assess_significance.R script
maxulysse Jan 20, 2021
5c0b818
fix: typo
maxulysse Jan 20, 2021
ad56acf
chores: update json schema
maxulysse Jan 20, 2021
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -91,6 +91,7 @@ Helpful contributors:
* [James A. Fellows Yates](https://github.com/jfy133)
* [Jesper Eisfeldt](https://github.com/J35P312)
* [Johannes Alneberg](https://github.com/alneberg)
* [José Fernández Navarro](https://github.com/jfnavarro)
* [Lucia Conde](https://github.com/lconde-ucl)
* [Malin Larsson](https://github.com/malinlarsson)
* [Marcel Martin](https://github.com/marcelm)
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12 changes: 11 additions & 1 deletion docs/usage.md
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Expand Up @@ -120,7 +120,7 @@ Specify the path to a specific config file (this is a core Nextflow command). Se

Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.

Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config:
Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `VEP` 32GB of memory, you could use the following config:

```nextflow
process {
Expand All @@ -130,6 +130,16 @@ process {
}
```

Alternatively, to give the workflow both processes `VEP` and `VEPmerge` 32GB of memory, you could use the following config:

```nextflow
process {
withLabel: VEP {
memory = 32.GB
}
}
```

See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.

If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition above). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
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10 changes: 2 additions & 8 deletions main.nf
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Expand Up @@ -3417,11 +3417,8 @@ process ControlFreecViz {

script:
"""
echo "Shaping CNV files to make sure we can assess significance"
LINEWIDTH=`head -1 ${cnvTumor}| wc -w`; awk 'NF=='$LINEWIDTH'{print}' ${cnvTumor} > TUMOR.CNVs

echo "############### Calculating significance values for TUMOR CNVs #############"
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args TUMOR.CNVs ${ratioTumor}
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}

echo "############### Creating graph for TUMOR ratios ###############"
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
Expand Down Expand Up @@ -3450,11 +3447,8 @@ process ControlFreecVizSingle {

script:
"""
echo "Shaping CNV files to make sure we can assess significance"
LINEWIDTH=`head -1 ${cnvTumor}| wc -w`; awk 'NF=='$LINEWIDTH'{print}' ${cnvTumor} > TUMOR.CNVs

echo "############### Calculating significance values for TUMOR CNVs #############"
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args TUMOR.CNVs ${ratioTumor}
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}

echo "############### Creating graph for TUMOR ratios ###############"
cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
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40 changes: 20 additions & 20 deletions nextflow_schema.json
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Expand Up @@ -19,14 +19,14 @@
"type": "string",
"fa_icon": "fas fa-dna",
"description": "Path to input file(s).",
"help_text": "Use this to specify the location of your input TSV file on `mapping`, `prepare_recalibration`, `recalibrate`, `variant_calling` and `Control-FREEC` steps (multiple files can be specified with quotes).\nIt can also be used to specify the path to a directory on `mapping` step with a single germline sample only.\nAlternatively, it can be used to specify the path to VCF input file on `annotate` step (multiple files can be specified with quotes).\n\n> **NB** "
"help_text": "Use this to specify the location of your input TSV file on `mapping`, `prepare_recalibration`, `recalibrate`, `variant_calling` and `Control-FREEC` steps (multiple files can be specified with quotes).\nIt can also be used to specify the path to a directory on `mapping` step with a single germline sample only.\nAlternatively, it can be used to specify the path to VCF input file on `annotate` step (multiple files can be specified with quotes)."
},
"step": {
"type": "string",
"default": "mapping",
"fa_icon": "fas fa-play",
"description": "The starting step.",
"help_text": "Only one step must be specified.\n> **NB** step can be specified with no concern for case, or the presence of `-` or `_`\n",
"description": "Starting step.",
"help_text": "Only one step.\n> **NB** step can be specified with no concern for case, or the presence of `-` or `_`\n",
"enum": [
"mapping",
"prepare_recalibration",
Expand All @@ -42,7 +42,8 @@
"default": "./results",
"fa_icon": "fas fa-folder-open"
}
}
},
"help_text": ""
},
"main_options": {
"title": "Main options",
Expand Down Expand Up @@ -100,7 +101,7 @@
"type": "string",
"fa_icon": "fas fa-forward",
"description": "Disable specified QC and Reporting tools.",
"help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_qc BaseRecalibrator` is actually just not saving the reports.\n> **NB** `--skip_qc MarkDuplicates` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.",
"help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_qc BaseRecalibrator` is actually just not saving the reports.\n> **NB** `--skip_qc MarkDuplicates` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.\n> **NB** tools can be specified with no concern for case, or the presence of `-` or `_`",
"enum": [
"null",
"all",
Expand Down Expand Up @@ -138,7 +139,7 @@
"fa_icon": "fas fa-cut",
"description": "Run Trim Galore.",
"hidden": true,
"help_text": "Use this to perform adapter trimming with Trim Galore.\ncf https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md"
"help_text": "Use this to perform adapter trimming with Trim Galore.\ncf [Trim Galore User Guide](https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md)"
},
"clip_r1": {
"type": "integer",
Expand Down Expand Up @@ -185,7 +186,7 @@
"type": "number",
"fa_icon": "fas fa-cut",
"description": "Specify how many reads should be contained in the split FastQ file",
"help_text": "Use the Nextflow splitFastq operator to specify how many reads should be contained in the split FASTQ file.\ncf https://www.nextflow.io/docs/latest/operator.html#splitfastq",
"help_text": "Use the Nextflow splitFastq operator to specify how many reads should be contained in the split FASTQ file.\ncf [splitfastq documentation](https://www.nextflow.io/docs/latest/operator.html#splitfastq)",
"hidden": true
}
}
Expand Down Expand Up @@ -214,7 +215,7 @@
"default": "-Xms4000m -Xmx7g",
"fa_icon": "fas fa-memory",
"description": "Establish values for GATK MarkDuplicates memory consumption",
"help_text": "See https://github.com/SciLifeLab/Sarek/pull/689",
"help_text": "See [SciLifeLab/Sarek/pull/689](https://github.com/SciLifeLab/Sarek/pull/689)",
"hidden": true
},
"use_gatk_spark": {
Expand All @@ -231,7 +232,7 @@
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip GATK MarkDuplicates",
"help_text": "This params will also save the mapped BAMS, to enable restart from step prepare_recalibration"
"help_text": "This params will also save the mapped BAMS, to enable restart from step `prepare_recalibration`"
}
}
},
Expand All @@ -247,14 +248,14 @@
"default": "null",
"fa_icon": "fas fa-wrench",
"description": "Overwrite ASCAT ploidy",
"help_text": "Requires that --ascat_purity is set"
"help_text": "Requires that `--ascat_purity` is set"
},
"ascat_purity": {
"type": "string",
"default": "null",
"fa_icon": "fas fa-wrench",
"description": "Overwrite ASCAT purity",
"help_text": "Requires that --ascat_ploidy is set"
"help_text": "Requires that `--ascat_ploidy` is set"
},
"cf_coeff": {
"type": "number",
Expand Down Expand Up @@ -289,7 +290,7 @@
"type": "string",
"fa_icon": "fas fa-file",
"description": "Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope",
"help_text": "Without PON, there will be no calls with PASS in the INFO field, only an unfiltered VCF is written.\nIt is recommended to make your own PON, as it depends on sequencer and library preparation.\nFor tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it should not be used as a real PON file.\n\nSee https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA\n> **NB** PON file should be bgzipped."
"help_text": "Without PON, there will be no calls with PASS in the INFO field, only an unfiltered VCF is written.\nIt is recommended to make your own PON, as it depends on sequencer and library preparation.\nFor tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it should not be used as a real PON file.\n\nSee [PON documentation](https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA)\n> **NB** PON file should be bgzipped."
},
"pon_index": {
"type": "string",
Expand All @@ -301,27 +302,27 @@
"type": "boolean",
"fa_icon": "fas fa-ban",
"description": "Do not analyze soft clipped bases in the reads for GATK Mutect2",
"help_text": "use the --dont-use-soft-clipped-bases params with GATK."
"help_text": "use the `--dont-use-soft-clipped-bases` params with GATK."
},
"umi": {
"type": "boolean",
"fa_icon": "fas fa-tape",
"description": "If provided, UMIs steps will be run to extract and annotate the reads with UMI and create consensus reads",
"help_text": "This part of the pipeline uses fgbio to convert the FASTQ files into a unmapped BAM, where reads are tagged with the UMIs extracted from the FASTQ sequences.\nIn order to allow the correct tagging, the UMI sequence must be contained in the read sequence itself, and not in the FASTQ filename.\nFollowing this step, the unmapped BAM is aligned and reads are then grouped based on mapping position and UMI tag.\nFinally, reads in the same groups are collapsed to create a consensus read.\nTo create consensus, we have chosen to use the adjacency method\n\ncf https://github.com/fulcrumgenomics/fgbio\ncf https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/\n\n> **NB** In order for the correct tagging to be performed, a read structure needs to be specified with --read_structure1 and --readstructure2"
"help_text": "This part of the pipeline uses fgbio to convert the FASTQ files into a unmapped BAM, where reads are tagged with the UMIs extracted from the FASTQ sequences.\nIn order to allow the correct tagging, the UMI sequence must be contained in the read sequence itself, and not in the FASTQ filename.\nFollowing this step, the unmapped BAM is aligned and reads are then grouped based on mapping position and UMI tag.\nFinally, reads in the same groups are collapsed to create a consensus read.\nTo create consensus, we have chosen to use the adjacency method\n\ncf [fgbio](https://github.com/fulcrumgenomics/fgbio)\ncf [UMIs, the problem, the solution and the proof](https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/)\n\n> **NB** In order for the correct tagging to be performed, a read structure needs to be specified with `--read_structure1` and `--readstructure2`"
},
"read_structure1": {
"type": "string",
"default": "null",
"fa_icon": "fas fa-clipboard-list",
"description": "When processing UMIs, a read structure should always be provided for each of the fastq files.",
"help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the fgbio documentation\ncf https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures"
"help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the [fgbio documentation](https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures)"
},
"read_structure2": {
"type": "string",
"default": "null",
"fa_icon": "fas fa-clipboard-list",
"description": "When processing UMIs, a read structure should always be provided for each of the fastq files.",
"help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the fgbio documentation\ncf https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures"
"help_text": "If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).\nThe read structure follows a format adopted by different tools and described in the [fgbio documentation](https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures)"
}
}
},
Expand Down Expand Up @@ -394,8 +395,7 @@
"type": "boolean",
"fa_icon": "fas fa-gavel",
"description": "Enable the use of the VEP GeneSplicer plugin.",
"hidden": true,
"help_text": "```bash\nnextflow run nf-core/sarek --step annotate --tools VEP --sample <file.vcf.gz> --genesplicer\n```"
"hidden": true
},
"snpeff_cache": {
"type": "string",
Expand Down Expand Up @@ -462,7 +462,7 @@
"type": "string",
"fa_icon": "fas fa-file",
"description": "Path to dbsnp index.",
"help_text": "> **NB** If none provided, will be generated automatically from the dbsnp file, if provided"
"help_text": "> **NB** If none provided, will be generated automatically from the dbsnp file."
},
"dict": {
"type": "string",
Expand Down Expand Up @@ -597,7 +597,7 @@
"description": "Workflow name.",
"fa_icon": "fas fa-fingerprint",
"hidden": true,
"help_text": "A custom name for the pipeline run. Unlike the core nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles."
"help_text": "A custom name for the pipeline run. Unlike the core Nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles."
},
"email": {
"type": "string",
Expand Down