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Merge pull request #35 from ewels/editor-config

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Editor config
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Phil Ewels 2020-07-11 14:20:37 +02:00 committed by GitHub
commit edd508487b
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39 changed files with 288 additions and 233 deletions
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11
.github/markdownlint.yml vendored Normal file
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@ -0,0 +1,11 @@
# Markdownlint configuration file
default: true,
line-length: false
no-multiple-blanks: 0
blanks-around-headers: false
blanks-around-lists: false
header-increment: false
no-duplicate-header:
siblings_only: true
ul-indent:
indent: 4

50
.github/workflows/lint-code.yml vendored Normal file
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@ -0,0 +1,50 @@
name: Lint Code
on: [push, pull_request]
jobs:
Markdown:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Run Markdownlint
run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install ECLint
run: npm install -g eclint
- name: Run ECLint check
run: eclint check $(git ls-files | grep -v test)
YAML:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v1
- name: Install NodeJS
uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")

1
README.md
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@ -5,6 +5,7 @@
A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl2.htmlhttps://www.nextflow.io/docs/edge/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
## Table of contents
* [Using existing modules](#using-existing-modules)
* [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage)

2
test-datasets

@ -1 +1 @@
Subproject commit aae85a5c9c72238959108212481ce83bae569709
Subproject commit ddbd0c4cf7f1721c78673c4dcc91fcd7940e67f8

6
tools/bowtie2/meta.yml
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@ -28,10 +28,10 @@ output:
- report:
type: file
description: mapping statistics report
pattern: *bowtie2_stats.txt
pattern: "*bowtie2_stats.txt"
- alignment:
type: file
description: alignment file in BAM format
pattern: *bowtie2.bam
pattern: "*bowtie2.bam"
authors:
- @FelixKrueger
- "@FelixKrueger"

6
tools/bwa/index/meta.yml
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@ -14,12 +14,12 @@ input:
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
pattern: "*.{fasta,fa}"
output:
-
- index:
type: file
description: bwa indexes file
pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
authors:
- @maxulysse
- "@maxulysse"

2
tools/bwa/mem/Dockerfile
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@ -5,5 +5,3 @@ LABEL authors="Jeremy Guntoro" \
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-bwa-mem/bin:$PATH

10
tools/bwa/mem/meta.yml
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@ -19,11 +19,11 @@ input:
- reads:
type: file
description: Input fastq file
pattern: *.{fastq,fq}
pattern: "*.{fastq,fq}"
- index:
type: file
description: bwa indexes file
pattern: *.{amb,ann,bwt,pac,sa}
pattern: "*.{amb,ann,bwt,pac,sa}"
- prefix:
type: val
description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
@ -32,11 +32,11 @@ output:
- bam:
type: file
description: Output bam file
pattern: *.bam
pattern: "*.bam"
- bamindex:
type: file
description: Output bam index file
pattern: *.bai
pattern: "*.bai"
authors:
- @jeremy1805
- "@jeremy1805"

2
tools/cutadapt/meta.yml
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@ -33,4 +33,4 @@ output:
type: file
description: trimmed FastQ file, or pair of files
authors:
- @piotr-faba-ardigen
- "@piotr-faba-ardigen"

6
tools/fastq_screen/meta.yml
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@ -25,7 +25,7 @@ output:
- report:
type: file
description: FastQ Screen report
pattern: *_screen.{txt,html,png}
optional_pattern: *_screen.bisulfite_orientation.png
pattern: "*_screen.{txt,html,png}"
optional_pattern: "*_screen.bisulfite_orientation.png"
authors:
- @FelixKrueger
- "@FelixKrueger"

7
tools/fastqc/meta.yml
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@ -27,8 +27,7 @@ output:
- report:
type: file
description: FastQC report
pattern: *_fastqc.{zip,html}
pattern: "*_fastqc.{zip,html}"
authors:
-
- @ewels
- @FelixKrueger
- "@ewels"
- "@FelixKrueger"

6
tools/gatk/dict/meta.yml
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@ -14,12 +14,12 @@ input:
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
pattern: "*.{fasta,fa}"
output:
-
- dict:
type: file
description: gatk dictionary file
pattern: *.{fasta,fa}.{dict}
pattern: "*.{fasta,fa}.{dict}"
authors:
- @maxulysse
- "@maxulysse"

6
tools/hisat2/meta.yml
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@ -28,10 +28,10 @@ output:
- report:
type: file
description: mapping statistics report
pattern: *hisat2_stats.txt
pattern: "*hisat2_stats.txt"
- alignment:
type: file
description: alignment file in BAM format
pattern: *hisat2.bam
pattern: "*hisat2.bam"
authors:
- @FelixKrueger
- "@FelixKrueger"

6
tools/htslib/tabix/meta.yml
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@ -15,12 +15,12 @@ input:
- input:
type: file
description: Input vcf.gz file
pattern: *.{vcf.gz}
pattern: "*.{vcf.gz}"
output:
-
- index:
type: file
description: tabix index file
pattern: *.{vcf.gz.tbi}
pattern: "*.{vcf.gz.tbi}"
authors:
- @maxulysse
- "@maxulysse"

4
tools/multiqc/meta.yml
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@ -21,6 +21,6 @@ output:
- multiqc_report:
type: file
description: MultiQC report
pattern: *multiqc*.html
pattern: "*multiqc*.html"
authors:
- @FelixKrueger
- "@FelixKrueger"

6
tools/samtools/faidx/meta.yml
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@ -16,12 +16,12 @@ input:
- input:
type: file
description: Input fasta file
pattern: *.{fasta,fa}
pattern: "*.{fasta,fa}"
output:
-
- faidx:
type: file
description: samtools index fasta file
pattern: *.fasta.fai
pattern: "*.fasta.fai"
authors:
- @maxulysse
- "@maxulysse"

6
tools/samtools/index/meta.yml
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@ -16,12 +16,12 @@ input:
- input:
type: file
description: Input BAM or CRAM file
pattern: *.{bam,cram}
pattern: "*.{bam,cram}"
output:
-
- index:
type: file
description: BAM or CRAM index file
pattern: *.{bai}
pattern: "*.{bai}"
authors:
- @ewels
- "@ewels"

6
tools/samtools/sort/meta.yml
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@ -16,12 +16,12 @@ input:
- input:
type: file
description: Input BAM or CRAM file
pattern: *.{bam,cram}
pattern: "*.{bam,cram}"
output:
-
- sorted_file:
type: file
description: Sorted BAM or CRAM file
pattern: *.{bam,cram}
pattern: "*.{bam,cram}"
authors:
- @ewels
- "@ewels"

2
tools/shovill/meta.yml
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@ -27,4 +27,4 @@ output:
description: fasta file
pattern: ${sample_id}.fasta
authors:
- @annacprice
- "@annacprice"

1
tools/tcoffee/main.nf
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@ -14,4 +14,3 @@ process tcoffee {
t_coffee -seq $fasta -outfile ${fasta}.aln
"""
}

6
tools/tcoffee/meta.yml
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@ -16,13 +16,13 @@ input:
- fasta:
type: path
description: Input fasta file
pattern: *.{fasta,fa,tfa}
pattern: "*.{fasta,fa,tfa}"
output:
-
- alignment:
type: file
description: tcoffee alignment file
pattern: *.aln
pattern: "*.aln"
authors:
- @JoseEspinosa
- "@JoseEspinosa"

1
tools/trim_galore/main.nf
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@ -98,4 +98,3 @@ process TRIM_GALORE {

9
tools/trim_galore/meta.yml
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@ -28,14 +28,13 @@ output:
- trimmed_fastq:
type: file
description: Trimmed FastQ files
pattern: *fq.gz
pattern: "*fq.gz"
-
- report:
type: file
description: Trim Galore! trimming report
pattern: *trimming_report.txt
pattern: "*trimming_report.txt"
authors:
-
- @ewels
- @FelixKrueger
- "@ewels"
- "@FelixKrueger"

11
tools/umi_tools/umi_tools.yml
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@ -31,16 +31,15 @@ processes:
- dedupBam:
type: tuple
description: A tuple of samples id and output bam file
pattern: [sample_id, *SAMPLE_ID.dedup.bam]
pattern: [sample_id, "*SAMPLE_ID.dedup.bam"]
- dedupBam:
type: tuple
description: A tuple of samples id and output bai file
pattern: [sample_id, *SAMPLE_ID.dedup.bam.bai]
pattern: [sample_id, "*SAMPLE_ID.dedup.bam.bai"]
- report:
type: file
description: Log file for the umi_tools operation
pattern: *SAMPLE_ID.dedup.log
pattern: "*SAMPLE_ID.dedup.log"
authors:
- @candiceh08
- @chris-cheshire
- "@candiceh08"
- "@chris-cheshire"