From 00c2e9a18bcea58ffff8b4bf9a911cecb4b59661 Mon Sep 17 00:00:00 2001 From: Sarah Griffiths Date: Fri, 11 Apr 2025 13:22:48 +0000 Subject: [PATCH] Fix aws/docker demo cmd [CW-5950] --- CHANGELOG.md | 1 + README.md | 4 ++-- docs/04_install_and_run.md | 2 +- docs/06_input_parameters.md | 2 +- nextflow.config | 4 ++-- nextflow_schema.json | 2 +- 6 files changed, 8 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5f1b4e6..6e48ff2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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. - 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`. +- 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. - Output the gene name annotated differential expression analysis count files only. - Only use full length reads in the differential expression analysis. diff --git a/README.md b/README.md index 7518757..fdb72c0 100644 --- a/README.md +++ b/README.md @@ -88,7 +88,7 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --direct_rna \ --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_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \ --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 | | 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 | | 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 | diff --git a/docs/04_install_and_run.md b/docs/04_install_and_run.md index 9dfc367..49a6b0c 100644 --- a/docs/04_install_and_run.md +++ b/docs/04_install_and_run.md @@ -49,7 +49,7 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --direct_rna \ --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_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \ --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \ diff --git a/docs/06_input_parameters.md b/docs/06_input_parameters.md index 62ba1fc..505fb2c 100644 --- a/docs/06_input_parameters.md +++ b/docs/06_input_parameters.md @@ -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 | | 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 | | 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 | diff --git a/nextflow.config b/nextflow.config index aadee65..b19d7bc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -43,7 +43,7 @@ params { cdna_kit = "SQK-PCS109" // Extra option passed to minimap2 when generating index - minimap2_index_opts = "-k14" + minimap2_index_opts = "-k 14" // Extra options passed to minimap2 // For SIRV data @@ -89,7 +89,7 @@ params { "--de_analysis", "--direct_rna", "--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_genome 'wf-transcriptomes-demo/hg38_chr20.fa'", "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'", diff --git a/nextflow_schema.json b/nextflow_schema.json index 8d44fa2..31282da 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -162,7 +162,7 @@ "type": "string", "title": "Minimap2 index options", "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." }, "minimap2_opts": {