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Update docs

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drpatelh 2020-10-15 11:13:54 +01:00
parent 7e2c7b1b41
commit 29f9b05433
13 changed files with 13 additions and 78 deletions
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7
software/SOFTWARE/TOOL/meta.yml
View file

@ -32,7 +32,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -49,11 +49,6 @@ input:
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
## TODO nf-core: Add a description of all of the variables used as output
output:
- meta:

7
software/bwa/index/meta.yml
View file

@ -24,7 +24,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -33,11 +33,6 @@ input:
- fasta:
type: file
description: Input genome fasta file
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- index:
type: file

7
software/bwa/mem/meta.yml
View file

@ -27,7 +27,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -50,11 +50,6 @@ input:
- fasta:
type: file
description: Input genome fasta file
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- bam:
type: file

7
software/fastqc/meta.yml
View file

@ -26,7 +26,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -42,11 +42,6 @@ input:
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/picard/collectmultiplemetrics/meta.yml
View file

@ -25,7 +25,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -43,11 +43,6 @@ input:
- fasta:
type: file
description: Genome fasta file
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/picard/markduplicates/meta.yml
View file

@ -25,7 +25,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -40,11 +40,6 @@ input:
type: file
description: BAM file
pattern: "*.{bam}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/picard/mergesamfiles/meta.yml
View file

@ -23,7 +23,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -38,11 +38,6 @@ input:
type: file
description: List of BAM files
pattern: "*.{bam}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/samtools/flagstat/meta.yml
View file

@ -27,7 +27,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -46,11 +46,6 @@ input:
type: file
description: Index for BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/samtools/idxstats/meta.yml
View file

@ -28,7 +28,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -47,11 +47,6 @@ input:
type: file
description: Index for BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/samtools/index/meta.yml
View file

@ -25,7 +25,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -40,11 +40,6 @@ input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/samtools/sort/meta.yml
View file

@ -25,7 +25,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -40,11 +40,6 @@ input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/samtools/stats/meta.yml
View file

@ -26,7 +26,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -45,11 +45,6 @@ input:
type: file
description: Index for BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map

7
software/trimgalore/meta.yml
View file

@ -24,7 +24,7 @@ params:
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- conda:
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
@ -60,11 +60,6 @@ input:
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- options:
type: map
description: |
Groovy Map containing module options for passing command-line arguments and
output file paths.
output:
- meta:
type: map