nf-core_modules/modules/isoseq3/cluster/meta.yml
Sébastien Guizard 1cf207a5b6
Update isoseq3/cluster (#856)
* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update code to new versions capture + better output channels

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* 👌 IMPROVE: Clean output file names + correct typo

* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster

* 🐛 FIX: Update output filename pattern

input filename and output filename were the same

* 👌 IMPROVE: Update meta.yml
2021-10-14 11:07:53 +01:00

81 lines
2.6 KiB
YAML

name: isoseq3_cluster
description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
keywords:
- cluster
tools:
- isoseq3:
description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
doi: ""
licence: ['BSD-3-clause-Clear']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- bam:
type: file
description: BAM file generated by isoseq3 refine
pattern: "*.bam"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "versions.yml"
- bam:
type: file
description: BAM file of clustered consensus
pattern: "*.transcripts.bam"
- pbi:
type: file
description: Pacbio Index of consensus reads generated by clustering
pattern: "*.transcripts.bam.pbi"
- cluster:
type: file
description: A two columns (from, to) file describing original read name to new read name
pattern: "*.transcripts.cluster"
- cluster_report:
type: file
description: A table files clusters (transcripts) members (read)
pattern: "*.transcripts.cluster_report.csv"
- transcriptset:
type: file
description: A metadata xml file which contains full paths to data files
pattern: "*.transcripts.transcriptset.xml"
- hq_bam:
type: file
description: High quality reads (when --use-qvs is set)
pattern: "*.transcripts.hq.bam"
- hq_pbi:
type: file
description: Pacbio index of high quality reads (when --use-qvs is set)
pattern: "*.transcripts.hq.bam.pbi"
- lq_bam:
type: file
description: Low quality reads (when --use-qvs is set)
pattern: "*.transcripts.lq.bam"
- lq_pbi:
type: file
description: Pacbio index of low quality reads (when --use-qvs is set)
pattern: "*.transcripts.lq.bam.pbi"
- singletons_bam:
type: file
description: Unclustered reads (when --singletons is set)
pattern: "*.transcripts.singletons.bam"
- singletons_pbi:
type: file
description: Pacbio index of unclustered reads (when --singletons is set)
pattern: "*.transcripts.singletons.bam.pbi"
authors:
- "@sguizard"