nf-core_modules/modules/gstama/collapse/meta.yml

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New module: `gstama/collapse` (#809) * 👌 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 gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Remove junk files * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 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 gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 IMPROVE: delete unnecessary files * 👌 IMPROVE: Update + clean - Remove unnecessary files - Update to new versions.yml file - Better output channels * 👌 IMPROVE: Update meta.yml and output channels * 👌 IMPROVE: Remove useless files * 👌 IMPROVE: Remove automatic MODE setup * 👌 IMPROVE: Applied @jfy133 code modification suggestions * Update modules/gstama/collapse/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 🐛 FIX: Add missing fasta option in meta.yml * 🐛 FIX: Fix typo * 🐛 FIX: Update package version * Update main.nf * Update meta.yml * Update modules/gstama/collapse/meta.yml * Apply suggestions from code review * Update tests/modules/gstama/collapse/main.nf * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 17:55:28 +00:00
name: GSTAMA_COLLAPSE
description: Collapse redundant transcript models in Iso-Seq data.
keywords:
- tama_collapse.py
- isoseq
- nanopore
- long-read
- transcriptome
- gene model
- TAMA
tools:
- tama_collapse.py:
description: Collapse similar gene model
homepage: https://github.com/sguizard/gs-tama
documentation: https://github.com/GenomeRIK/tama/wiki
tool_dev_url: https://github.com/sguizard/gs-tama
doi: 10.1186/s12864-020-07123-7
licence: GNU GPL3
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- bam:
type: file
description: A sorted BAM or sam file of aligned reads
pattern: "*.{bam,sam}"
- fasta:
type: file
description: A fasta file of the genome used for the mapping
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bed:
type: file
description: a bed12 format file containing the final collapsed version of your transcriptome
pattern: "*.bed"
- bed_trans_reads:
type: file
description: This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models.
pattern: "*_trans_read.bed"
- local_density_error:
type: file
description: This file contains the log of filtering for local density error around the splice junctions ("-lde")
pattern: "*_local_density_error.txt"
- polya:
type: file
description: This file contains the reads with potential poly A truncation.
pattern: "*_polya.txt"
- read:
type: file
description: This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file
pattern: "*_read.txt"
- strand_check:
type: file
description: This file shows instances where the sam flag strand information contrasted the GMAP strand information.
pattern: "*_strand_check.txt"
- trans_report:
type: file
description: This file contains collapsing information for each transcript.
pattern: "*_trans_report.txt"
- varcov:
type: file
description: This file contains the coverage information for each variant detected.
pattern: "*_varcov.txt"
- variants:
type: file
description: This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.
pattern: "*_variants.txt"
authors:
- "@sguizard"