kfukuta/wf-transcriptomes-v202
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Sarah Griffiths 2023-12-07 14:05:02 +00:00
parent 2580c99ae4
commit ed847d9a1f
8 changed files with 31 additions and 20 deletions
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2
.pre-commit-config.yaml
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@ -8,7 +8,7 @@ repos:
always_run: true
pass_filenames: false
additional_dependencies:
- epi2melabs>=0.0.49
- epi2melabs>=0.0.50
- 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

5
CHANGELOG.md
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@ -4,10 +4,13 @@ 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]
## [v1.0.0]
### Added
- Published minimap2 and pychopper results to output directory.
- Two extra pychopper parameters `--cdna_kit` and `--pychopper_backend`. `--pychopper_options` is still available to define any other options.
- Memory requirements for each process.
### Changed
- Documentation.
## [v0.4.2]
### Changed

6
README.md
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@ -163,13 +163,13 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec
## Outputs
Outputs files may be aggregated including information for all samples or provided per sample. Per sample files will be prefixed with respective aliases and represented below as {{ alias }}.
Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
| Title | File path | Description | Per sample or aggregated |
|-------|-----------|-------------|--------------------------|
| workflow report | wf-transcriptomes-report.html | a HTML report document detailing the primary findings of the workflow | aggregated |
| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
| Read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
| Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
| Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
| Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
@ -180,7 +180,7 @@ Outputs files may be aggregated including information for all sample
| Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions . | aggregated |
| Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
| Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential gene expression report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
| Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |

6
docs/07_outputs.md
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@ -1,10 +1,10 @@
Outputs files may be aggregated including information for all samples or provided per sample. Per sample files will be prefixed with respective aliases and represented below as {{ alias }}.
Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
| Title | File path | Description | Per sample or aggregated |
|-------|-----------|-------------|--------------------------|
| workflow report | wf-transcriptomes-report.html | a HTML report document detailing the primary findings of the workflow | aggregated |
| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
| Read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
| Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
| Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
| Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
@ -15,7 +15,7 @@ Outputs files may be aggregated including information for all sample
| Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions . | aggregated |
| Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
| Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential gene expression report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
| Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
| Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
| Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |

4
lib/NfcoreSchema.groovy
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@ -141,7 +141,7 @@ class NfcoreSchema {
for (specifiedParam in params.keySet()) {
// nextflow params
if (nf_params.contains(specifiedParam)) {
log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
log.error "You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
has_error = true
}
// unexpected params
@ -180,7 +180,7 @@ class NfcoreSchema {
schema.validate(params_json)
} catch (ValidationException e) {
println ''
log.error 'ERROR: Validation of pipeline parameters failed!'
log.error 'Validation of pipeline parameters failed!'
JSONObject exceptionJSON = e.toJSON()
HashSet<String> observed_exceptions = []
printExceptions(exceptionJSON, params_json, log, enums, raw_schema, observed_exceptions)

8
lib/ingress.nf
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@ -240,6 +240,7 @@ process checkBamHeaders {
label "ingress"
label "wf_common"
cpus 1
memory "2 GB"
input: tuple val(meta), path("input_dir/reads*.bam")
output:
// set the two env variables by `eval`-ing the output of the python script
@ -257,6 +258,7 @@ process mergeBams {
label "ingress"
label "wf_common"
cpus 3
memory "4 GB"
input: tuple val(meta), path("input_bams/reads*.bam")
output: tuple val(meta), path("reads.bam")
shell:
@ -271,6 +273,7 @@ process catSortBams {
label "ingress"
label "wf_common"
cpus 4
memory "4 GB"
input: tuple val(meta), path("input_bams/reads*.bam")
output: tuple val(meta), path("reads.bam")
script:
@ -285,6 +288,7 @@ process sortBam {
label "ingress"
label "wf_common"
cpus 3
memory "4 GB"
input: tuple val(meta), path("reads.bam")
output: tuple val(meta), path("reads.sorted.bam")
script:
@ -298,6 +302,7 @@ process bamstats {
label "ingress"
label "wf_common"
cpus 3
memory "4 GB"
input:
tuple val(meta), path("reads.bam")
output:
@ -414,6 +419,7 @@ process move_or_compress_fq_file {
label "ingress"
label "wf_common"
cpus 1
memory "2 GB"
input:
// don't stage `input` with a literal because we check the file extension
tuple val(meta), path(input)
@ -439,6 +445,7 @@ process fastcat {
label "ingress"
label "wf_common"
cpus 3
memory "2 GB"
input:
tuple val(meta), path("input")
val extra_args
@ -737,6 +744,7 @@ process validate_sample_sheet {
cpus 1
label "ingress"
label "wf_common"
memory "2 GB"
input:
path "sample_sheet.csv"
val required_sample_types

14
nextflow.config
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@ -92,12 +92,12 @@ params {
wf {
example_cmd = [
"--fastq 'differential_expression/differential_expression_fastq'",
"--de_analysis --ref_genome 'differential_expression/hg38_chr20.fa'" ,
"--transcriptome-source 'reference-guided'",
"--ref_annotation 'differential_expression/gencode.v22.annotation.chr20.gtf'",
"--direct_rna --minimap2_index_opts '-k 15' --sample_sheet 'differential_expression/sample_sheet.csv'",
"--jaffal_refBase 'differential_expression/chr20/' --jaffal_genome 'hg38_chr20' --jaffal_annotation 'genCode22'"
"--condition_sheet 'wf-transcriptomes-demo/condition_sheet.tsv'",
"--direct_rna",
"--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
"--minimap2_index_opts '-k15'",
"--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
"--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
]
agent = null
container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"
@ -112,7 +112,7 @@ manifest {
description = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
mainScript = 'main.nf'
nextflowVersion = '>=23.04.2'
version = 'v0.4.2'
version = 'v1.0.0'
}
epi2melabs {

4
output_definition.json
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@ -18,7 +18,7 @@
},
"read-stats-per-read": {
"filepath": "fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv",
"title": "Per file read stats",
"title": "Read stats",
"description": "A TSV with per read stats, including all samples.",
"mime-type": "text/tab-separated-values",
"optional": false,
@ -106,7 +106,7 @@
},
"dtu-report-pdf": {
"filepath": "/de_analysis/results_dtu.pdf",
"title": "Differential gene expression report",
"title": "Differential transcript usage report",
"description": "Summary report of differential transcript usage results as a PDF.",
"mime-type": "application/pdf",
"optional": true,