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Fix aws/docker demo cmd [CW-5950]

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Sarah Griffiths 2025-04-11 13:22:48 +00:00
parent cd97c1398e
commit 00c2e9a18b
6 changed files with 8 additions and 7 deletions
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1
CHANGELOG.md
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@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `all_gene_counts.tsv` contained the DE counts results. - `all_gene_counts.tsv` contained the DE counts results.
- Reduced memory usage of the report workflow process. - Reduced memory usage of the report workflow process.
- Output BAM alignments in all cases unless the workflow is run with `transcriptome_source` set to `precomputed`. - Output BAM alignments in all cases unless the workflow is run with `transcriptome_source` set to `precomputed`.
- Corrected the demo command in the `README.md`.
- The merged transcriptome generated for differential expression analysis now only contains the exons and not the full genomic sequence. - The merged transcriptome generated for differential expression analysis now only contains the exons and not the full genomic sequence.
- Output the gene name annotated differential expression analysis count files only. - Output the gene name annotated differential expression analysis count files only.
- Only use full length reads in the differential expression analysis. - Only use full length reads in the differential expression analysis.

4
README.md
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@ -88,7 +88,7 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--direct_rna \ --direct_rna \
--fastq 'wf-transcriptomes-demo/differential_expression_fastq' \ --fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
--minimap2_index_opts '-k15' \ --minimap2_index_opts '-k 15' \
--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \ --ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \ --ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \ --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
@ -170,7 +170,7 @@ input_reads.fastq ─── input_directory ─── input_directory
|--------------------------|------|-------------|------|---------| |--------------------------|------|-------------|------|---------|
| plot_gffcmp_stats | boolean | Create a PDF of plots from showing gffcompare results | If set to true, a PDF file containing detailed gffcompare reults will be output | True | | plot_gffcmp_stats | boolean | Create a PDF of plots from showing gffcompare results | If set to true, a PDF file containing detailed gffcompare reults will be output | True |
| gffcompare_opts | string | Extra command-line options to give to gffcompare -r | For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). | -R | | gffcompare_opts | string | Extra command-line options to give to gffcompare -r | For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). | -R |
| minimap2_index_opts | string | Extra command-line options for minimap2 indexing. | See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly. | -k14 | | minimap2_index_opts | string | Extra command-line options for minimap2 indexing. | See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly. | -k 14 |
| minimap2_opts | string | Additional command-line options for minimap2 alignment. | See [minimap2 options](https://lh3.github.io/minimap2/minimap2.html#5) for further information. These will only be relevant in the reference based transcriptome assembly. | -uf | | minimap2_opts | string | Additional command-line options for minimap2 alignment. | See [minimap2 options](https://lh3.github.io/minimap2/minimap2.html#5) for further information. These will only be relevant in the reference based transcriptome assembly. | -uf |
| minimum_mapping_quality | integer | filter aligned reads by MAPQ quality. | Reads that do not meet this mapping quality after minimap2 alignment, will be filtered out. | 40 | | minimum_mapping_quality | integer | filter aligned reads by MAPQ quality. | Reads that do not meet this mapping quality after minimap2 alignment, will be filtered out. | 40 |
| stringtie_opts | string | Extra command-line options for stringtie transcript assembly. | For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options). | --conservative | | stringtie_opts | string | Extra command-line options for stringtie transcript assembly. | For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options). | --conservative |

2
docs/04_install_and_run.md
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@ -49,7 +49,7 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--direct_rna \ --direct_rna \
--fastq 'wf-transcriptomes-demo/differential_expression_fastq' \ --fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
--minimap2_index_opts '-k15' \ --minimap2_index_opts '-k 15' \
--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \ --ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \ --ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \ --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \

2
docs/06_input_parameters.md
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@ -34,7 +34,7 @@
|--------------------------|------|-------------|------|---------| |--------------------------|------|-------------|------|---------|
| plot_gffcmp_stats | boolean | Create a PDF of plots from showing gffcompare results | If set to true, a PDF file containing detailed gffcompare reults will be output | True | | plot_gffcmp_stats | boolean | Create a PDF of plots from showing gffcompare results | If set to true, a PDF file containing detailed gffcompare reults will be output | True |
| gffcompare_opts | string | Extra command-line options to give to gffcompare -r | For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). | -R | | gffcompare_opts | string | Extra command-line options to give to gffcompare -r | For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). | -R |
| minimap2_index_opts | string | Extra command-line options for minimap2 indexing. | See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly. | -k14 | | minimap2_index_opts | string | Extra command-line options for minimap2 indexing. | See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly. | -k 14 |
| minimap2_opts | string | Additional command-line options for minimap2 alignment. | See [minimap2 options](https://lh3.github.io/minimap2/minimap2.html#5) for further information. These will only be relevant in the reference based transcriptome assembly. | -uf | | minimap2_opts | string | Additional command-line options for minimap2 alignment. | See [minimap2 options](https://lh3.github.io/minimap2/minimap2.html#5) for further information. These will only be relevant in the reference based transcriptome assembly. | -uf |
| minimum_mapping_quality | integer | filter aligned reads by MAPQ quality. | Reads that do not meet this mapping quality after minimap2 alignment, will be filtered out. | 40 | | minimum_mapping_quality | integer | filter aligned reads by MAPQ quality. | Reads that do not meet this mapping quality after minimap2 alignment, will be filtered out. | 40 |
| stringtie_opts | string | Extra command-line options for stringtie transcript assembly. | For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options). | --conservative | | stringtie_opts | string | Extra command-line options for stringtie transcript assembly. | For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options). | --conservative |

4
nextflow.config
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@ -43,7 +43,7 @@ params {
cdna_kit = "SQK-PCS109" cdna_kit = "SQK-PCS109"
// Extra option passed to minimap2 when generating index // Extra option passed to minimap2 when generating index
minimap2_index_opts = "-k14" minimap2_index_opts = "-k 14"
// Extra options passed to minimap2 // Extra options passed to minimap2
// For SIRV data // For SIRV data
@ -89,7 +89,7 @@ params {
"--de_analysis", "--de_analysis",
"--direct_rna", "--direct_rna",
"--fastq 'wf-transcriptomes-demo/differential_expression_fastq'", "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
"--minimap2_index_opts '-k15'", "--minimap2_index_opts '-k 15'",
"--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'", "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
"--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'", "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
"--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'", "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",

2
nextflow_schema.json
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@ -162,7 +162,7 @@
"type": "string", "type": "string",
"title": "Minimap2 index options", "title": "Minimap2 index options",
"description": "Extra command-line options for minimap2 indexing.", "description": "Extra command-line options for minimap2 indexing.",
"default": "-k14", "default": "-k 14",
"help_text": "See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly." "help_text": "See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly."
}, },
"minimap2_opts": { "minimap2_opts": {