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Merge pull request #370 from drpatelh/fixes
Fix #368
2 parents 6b23e8c + e5d5293 commit 5daf5a8

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+85
-58
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‎CHANGELOG.md

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@@ -11,6 +11,8 @@ Special thanks to the following for their code contributions to the release:
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- [Friederike Hanssen](https://github.com/FriederikeHanssen)
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- [Hugo Tavares](https://github.com/tavareshugo)
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- [James Fellows Yates](https://github.com/jfy133)
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- [Jessica Wu](https://github.com/wutron)
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- [Matthew Wells](https://github.com/mattheww95)
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- [Maxime Garcia](https://github.com/maxulysse)
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- [Phil Ewels](https://github.com/ewels)
@@ -30,6 +32,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
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- [[#348](https://github.com/nf-core/viralrecon/issues/348)] - Document full parameters of iVar consensus
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- [[#349](https://github.com/nf-core/viralrecon/issues/349)] - ERROR in Script plasmidID
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- [[#356](https://github.com/nf-core/viralrecon/issues/356)] - Add NEB SARS-CoV-2 primers
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- [[#368](https://github.com/nf-core/viralrecon/issues/368)] - Incorrect depth from ivar variants reported in variants long table
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- Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
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- Add `tower.yml` for Report rendering in Nextflow Tower
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- Use `--skip_plasmidid` by default

‎README.md

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@@ -102,6 +102,8 @@ A number of improvements were made to the pipeline recently, mainly with regard
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4. Start running your own analysis!
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> - Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration except for parameters; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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- Typical command for Illumina shotgun analysis:
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```bash

‎bin/ivar_variants_to_vcf.py

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@@ -126,7 +126,7 @@ def parse_ivar_line(line):
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QUAL = "."
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## Determine FILTER field
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INFO = f"DP={line[11]}"
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INFO = f"DP={int(float(line[11]))}"
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pass_test = line[13]
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return (

‎conf/modules_illumina.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).

‎conf/modules_nanopore.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).

‎conf/test_full_nanopore.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running full-size tests
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a full size pipeline test.
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Use as follows:

‎conf/test_full_sispa.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running full-size tests
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a full size pipeline test.
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Use as follows:

‎conf/test_nanopore.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:

‎conf/test_sispa.config

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/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:

‎docs/usage.md

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> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
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## Pipeline parameters
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Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration except for parameters; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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## Samplesheet format
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### Illumina

‎lib/NfcoreTemplate.groovy

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}
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}
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//
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// Warn if using custom configs to provide pipeline parameters
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//
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public static void warnParamsProvidedInConfig(workflow, log) {
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if (workflow.configFiles.size() > 1) {
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Multiple config files detected!\n" +
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" Please provide pipeline parameters via the CLI or Nextflow '-params-file' option.\n" +
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" Custom config files including those provided by the '-c' Nextflow option can be\n" +
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" used to provide any configuration except for parameters.\n\n" +
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" Docs: https://nf-co.re/usage/configuration#custom-configuration-files\n" +
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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}
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}
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//
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// Generate version string
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//

‎lib/Utils.groovy

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}
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if (channels_missing | channel_priority_violation) {
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" There is a problem with your Conda configuration!\n\n" +
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" You will need to set-up the conda-forge and bioconda channels correctly.\n" +
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" Please refer to https://bioconda.github.io/\n" +
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" The observed channel order is \n" +
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" ${channels}\n" +
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" but the following channel order is required:\n" +
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" ${required_channels_in_order}\n" +
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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}
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}
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}

‎lib/WorkflowCommons.groovy

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//
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private static void genomeExistsError(params, log) {
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if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
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log.error "=============================================================================\n" +
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log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
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" Currently, the available genome keys are:\n" +
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" ${params.genomes.keySet().join(", ")}\n" +
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"============================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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System.exit(1)
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}
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}
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)
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}
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if (total != (left + right)) {
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log.warn "=============================================================================\n" +
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Please check the name field (column 4) in the file supplied via --primer_bed.\n\n" +
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" All of the values in that column do not end with those supplied by:\n" +
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" --primer_left_suffix : $primer_left_suffix\n" +
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" --primer_right_suffix: $primer_right_suffix\n\n" +
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" This information is required to collapse the primer intervals into amplicons\n" +
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" for the coverage plots generated by the pipeline.\n" +
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"==================================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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}
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}
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def intersect = bed_contigs.intersect(fai_contigs)
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if (intersect.size() != bed_contigs.size()) {
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def diff = bed_contigs.minus(intersect).sort()
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log.error "=============================================================================\n" +
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log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Contigs in primer BED file do not match those in the reference genome:\n\n" +
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" ${diff.join('\n ')}\n\n" +
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" Please check:\n" +
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" - Primer BED file supplied with --primer_bed\n" +
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" - Genome FASTA file supplied with --fasta\n" +
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"============================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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System.exit(1)
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}
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}

‎lib/WorkflowIllumina.groovy

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if (line.contains('>')) {
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count++
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if (count > 1) {
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log.warn "=============================================================================\n" +
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" This pipeline does not officially support multi-fasta genome files!\n\n" +
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" The parameters and processes are tailored for viral genome analysis.\n" +
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" Please amend the '--fasta' parameter.\n" +
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"==================================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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break
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}
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}
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if (name.contains(name_prefix)) {
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count++
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if (count > 1) {
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log.warn "=============================================================================\n" +
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log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Found '${name_prefix}' in the name field of the primer BED file!\n" +
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" This suggests that you have used the SWIFT/SNAP protocol to prep your samples.\n" +
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" If so, please set '--ivar_trim_offset 5' as suggested in the issue below:\n" +
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" https://github.com/nf-core/viralrecon/issues/170\n" +
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"==================================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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break
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}
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}

‎lib/WorkflowMain.groovy

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// Print parameter summary log to screen
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log.info paramsSummaryLog(workflow, params, log)
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// Warn about using custom configs to provide pipeline parameters
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NfcoreTemplate.warnParamsProvidedInConfig(workflow, log)
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// Validate workflow parameters via the JSON schema
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if (params.validate_params) {
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NfcoreSchema.validateParameters(workflow, params, log)
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" - https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config\n\n" +
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" If you would still like to blame us please come and find us on nf-core Slack:\n" +
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" - https://nf-co.re/viralrecon#contributions-and-support\n" +
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"============================================================================="
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
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def genome_map = params.genomes[ params.genome ]
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if (primer_set) {
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if (genome_map.containsKey(primer_set_version)) {
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genome_map = genome_map[ primer_set_version ]
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} else {
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log.error "=============================================================================\n" +
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log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" --primer_set_version '${primer_set_version}' not found!\n\n" +
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" Currently, the available primer set version keys are: ${genome_map.keySet().join(", ")}\n\n" +
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" Please check:\n" +
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System.exit(1)
129132
}
130133
} else {
131-
log.error "=============================================================================\n" +
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log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" --primer_set '${primer_set}' not found!\n\n" +
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" Currently, the available primer set keys are: ${genome_map.keySet().join(", ")}\n\n" +
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" Please check:\n" +
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138141
System.exit(1)
139142
}
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} else {
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log.error "=============================================================================\n" +
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log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Genome '${params.genome}' does not contain any primer sets!\n\n" +
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" Please check:\n" +
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" - The value provided to --genome (currently '${params.genome}')\n" +

‎workflows/illumina.nf

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/*
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========================================================================================
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VALIDATE INPUTS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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def valid_params = [
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3434
if (!variant_caller) { variant_caller = params.protocol == 'amplicon' ? 'ivar' : 'bcftools' }
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3636
/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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CONFIG FILES
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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ch_multiqc_config = file("$projectDir/assets/multiqc_config_illumina.yml", checkIfExists: true)
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4747
ch_ivar_variants_header_mqc = file("$projectDir/assets/headers/ivar_variants_header_mqc.txt", checkIfExists: true)
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4949
/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IMPORT LOCAL MODULES/SUBWORKFLOWS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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5555
//
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7777
include { FASTQ_TRIM_FASTP_FASTQC } from '../subworkflows/local/fastq_trim_fastp_fastqc'
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7979
/*
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========================================================================================
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8181
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82+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8383
*/
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8585
//
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9797
// SUBWORKFLOW: Consisting entirely of nf-core/modules
9898
//
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include { FASTQ_ALIGN_BOWTIE2 } from '../subworkflows/nf-core/fastq_align_bowtie2/main'
100-
include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_markduplicates_picard'
100+
include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_markduplicates_picard/main'
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102102
/*
103-
========================================================================================
103+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
104104
RUN MAIN WORKFLOW
105-
========================================================================================
105+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
106106
*/
107107

108108
// Info required for completion email and summary
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645645
}
646646

647647
/*
648-
========================================================================================
648+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
649649
COMPLETION EMAIL AND SUMMARY
650-
========================================================================================
650+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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653653
workflow.onComplete {
@@ -658,7 +658,7 @@ workflow.onComplete {
658658
}
659659

660660
/*
661-
========================================================================================
661+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
662662
THE END
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========================================================================================
663+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664664
*/

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