kfukuta/wf-transcriptomes-v202
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Remove unused parameter

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This commit is contained in:
Neil Horner 2023-07-26 21:09:29 +00:00 committed by Sarah Griffiths
parent e56aefe7db
commit 285e7c8ecf
3 changed files with 13 additions and 11 deletions
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6
.gitlab-ci.yml
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@ -89,7 +89,7 @@ docker-run:
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
--direct_rna --minimap_index_opts '-k 15' \ --direct_rna --minimap_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
@ -103,7 +103,7 @@ docker-run:
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \
--direct_rna --minimap_index_opts '-k 15' \ --direct_rna --minimap_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
@ -117,7 +117,7 @@ docker-run:
--ref_genome differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \ --ref_genome differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
--ref_annotation differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \ --ref_annotation differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
--direct_rna --minimap_index_opts '-w 25' \ --direct_rna --minimap_index_opts '-w 25' \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts, preprocess_reads,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam

9
README.md
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@ -241,7 +241,8 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 --direct_rna --minimap_index_opts \
-k15
``` ```
You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false. You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
eg. eg.
@ -251,9 +252,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 \ --direct_rna --minimap_index_opts \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ -k15 \
--transcriptome_assembly false --ref_transcriptome differential_expression/ref_transcriptome.fasta
``` ```
## Workflow outputs ## Workflow outputs

9
docs/quickstart.md
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@ -151,7 +151,8 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 --direct_rna --minimap_index_opts \
-k15
``` ```
You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false. You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
eg. eg.
@ -161,9 +162,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 \ --direct_rna --minimap_index_opts \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ -k15 \
--transcriptome_assembly false --ref_transcriptome differential_expression/ref_transcriptome.fasta
``` ```
## Workflow outputs ## Workflow outputs