Actually output the dexseq file
This commit is contained in:
Sarah Griffiths
parent
45a717aaf3
commit
465d060933
@ -11,7 +11,7 @@ repos:
|
||||
- epi2melabs==0.0.57
|
||||
- id: build_models
|
||||
name: build_models
|
||||
entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py
|
||||
entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-subclass-enum --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py
|
||||
language: python
|
||||
files: 'results_schema.yml'
|
||||
pass_filenames: false
|
||||
|
||||
@ -4,11 +4,12 @@ All notable changes to this project will be documented in this file.
|
||||
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
|
||||
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
||||
|
||||
## [Unreleased]
|
||||
## [v1.5.0]
|
||||
### Updated
|
||||
- Workflow report updated to use `ezcharts`.
|
||||
### Fixed
|
||||
- Exons per isoforms histogram reporting incorrect numbers.
|
||||
- Output the `results_dexseq.tsv` file when `--de_analysis` enabled.
|
||||
### Removed
|
||||
- per-class gffcompare tracking files as there exists a combine tracking file.
|
||||
|
||||
|
||||
@ -232,7 +232,7 @@ Output files may be aggregated including information for all samples or provided
|
||||
| Transcript per million counts | de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated |
|
||||
| Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
|
||||
| Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
|
||||
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated |
|
||||
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated |
|
||||
| Index of reference FASTA file | igv_reference/{{ ref_genome file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated |
|
||||
| GZI index of the reference FASTA file | igv_reference/{{ ref_genome file }}.gzi | GZI Index of the reference FASTA file. | aggregated |
|
||||
| JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated |
|
||||
|
||||
@ -25,7 +25,7 @@ Output files may be aggregated including information for all samples or provided
|
||||
| Transcript per million counts | de_analysis/unfiltered_tpm_transcript_counts.tsv | This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples. | aggregated |
|
||||
| Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
|
||||
| Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
|
||||
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. | aggregated |
|
||||
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated |
|
||||
| Index of reference FASTA file | igv_reference/{{ ref_genome file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated |
|
||||
| GZI index of the reference FASTA file | igv_reference/{{ ref_genome file }}.gzi | GZI Index of the reference FASTA file. | aggregated |
|
||||
| JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated |
|
||||
|
||||
2
main.nf
2
main.nf
@ -257,7 +257,7 @@ process assemble_transcripts{
|
||||
|
||||
"""
|
||||
stringtie --rf ${G_FLAG} -L -v -p ${task.cpus} ${params.stringtie_opts} \
|
||||
-o ${prefix}.gff -l ${prefix} ${bam} 2>/dev/null
|
||||
-o ${prefix}.gff -l ${prefix} ${bam}
|
||||
"""
|
||||
}
|
||||
|
||||
|
||||
@ -106,7 +106,7 @@ manifest {
|
||||
description = 'Transcriptome analysis including differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '>=23.04.2'
|
||||
version = 'v1.4.0'
|
||||
version = 'v1.5.0'
|
||||
}
|
||||
|
||||
epi2melabs {
|
||||
|
||||
@ -187,7 +187,7 @@
|
||||
"final_non_redundant_transcriptome": {
|
||||
"filepath": "de_analysis/final_non_redundant_transcriptome.fasta",
|
||||
"title": "Final non redundant transcriptome",
|
||||
"description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.",
|
||||
"description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided.",
|
||||
"mime-type": "text/x-fasta",
|
||||
"optional": true,
|
||||
"type": "aggregated"
|
||||
|
||||
@ -165,7 +165,7 @@ workflow differential_expression {
|
||||
de_report = analysis.flt_counts.concat(analysis.gene_counts, analysis.dge, analysis.dexseq,
|
||||
analysis.stageR, sample_sheet, merged, ref_annotation, merged_TPM, analysis.unflt_counts).collect()
|
||||
// Concat files required to be output to user without any changes
|
||||
de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, analysis.dge_pdf, analysis.dge_tsv,
|
||||
de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, analysis.dge_pdf, analysis.dge_tsv, analysis.dexseq,
|
||||
analysis.dtu_gene, analysis.dtu_transcript, analysis.dtu_stageR, analysis.dtu_pdf, analysis.flt_counts, analysis.gene_counts, merged_TPM).collect()
|
||||
count_transcripts_file = count_transcripts.out.seqkit_stats.collect()
|
||||
emit:
|
||||
|
||||
Loading…
Reference in New Issue
Block a user