kfukuta/wf-transcriptomes-v202
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Merge branch 'resource-updates' into 'dev'

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Resource updates

Closes CW-3362

See merge request epi2melabs/workflows/wf-transcriptomes!156
This commit is contained in:
Sarah Griffiths 2024-02-12 10:20:04 +00:00
commit f025538f17
7 changed files with 47 additions and 35 deletions
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55
.gitlab-ci.yml
View File

@ -4,13 +4,14 @@ include:
file: "wf-containers.yaml" file: "wf-containers.yaml"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis --ref_genome differential_expression/hg38_chr20.fa \ --de_analysis --ref_genome differential_expression/hg38_chr20.fa \
--transcriptome-source reference-guided \ --transcriptome-source reference-guided \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet differential_expression/sample_sheet.csv \ --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" --jaffal_refBase differential_expression/chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
-c demo.nextflow.config"
CI_FLAVOUR: "new" CI_FLAVOUR: "new"
macos-run: macos-run:
@ -62,35 +63,39 @@ docker-run:
when: never when: never
- if: $MATRIX_NAME == "isoforms" - if: $MATRIX_NAME == "isoforms"
variables: variables:
NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm" --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
-c demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "no_ref_annotation" - if: $MATRIX_NAME == "no_ref_annotation"
variables: variables:
NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
--ref_genome chr20/hg38_chr20.fa" --ref_genome chr20/hg38_chr20.fa \
-c demo.nextflow.config"
NF_IGNORE_PROCESSES: run_gffcompare,preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: run_gffcompare,preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "fusions" - if: $MATRIX_NAME == "fusions"
variables: variables:
NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \ --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22" --jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22 \
-c demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "differential_expression" - if: $MATRIX_NAME == "differential_expression"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \ --ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet differential_expression/sample_sheet.csv" --direct_rna --minimap2_index_opts '-k 15' --sample_sheet differential_expression/sample_sheet.csv \
-c demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "only_differential_expression" - if: $MATRIX_NAME == "only_differential_expression"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \ --transcriptome-source precomputed \
--de_analysis \ --de_analysis \
@ -98,13 +103,14 @@ docker-run:
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
--direct_rna --minimap2_index_opts '-k 15' \ --direct_rna --minimap2_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
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,decompress_transcriptome,preprocess_ref_transcriptome build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "differential_expression_gff3" - if: $MATRIX_NAME == "differential_expression_gff3"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \ --transcriptome-source precomputed \
--de_analysis \ --de_analysis \
@ -112,13 +118,14 @@ docker-run:
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \
--direct_rna --minimap2_index_opts '-k 15' \ --direct_rna --minimap2_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
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,decompress_transcriptome,preprocess_ref_transcriptome build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "ncbi_gzip" - if: $MATRIX_NAME == "ncbi_gzip"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \ NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression_ncbi/differential_expression_fastq \ --fastq differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed \ --transcriptome-source precomputed \
@ -126,46 +133,50 @@ 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 --minimap2_index_opts '-w 25' \ --direct_rna --minimap2_index_opts '-w 25' \
--sample_sheet test_data/sample_sheet.csv" --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
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,decompress_transcriptome,preprocess_ref_transcriptome build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "ncbi_no_gene_id" - if: $MATRIX_NAME == "ncbi_no_gene_id"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \ NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression_ncbi/differential_expression_fastq \ --fastq differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome-source precomputed --de_analysis \
--ref_genome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \ --ref_genome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
--ref_annotation differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \ --ref_annotation differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
--direct_rna --ref_transcriptome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \ --direct_rna --ref_transcriptome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
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,decompress_transcriptome,preprocess_ref_transcriptome build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "ensembl_with_versions" - if: $MATRIX_NAME == "ensembl_with_versions"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \ NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression/differential_expression_fastq \ --fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome-source precomputed --de_analysis \
--ref_genome differential_expression/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \ --ref_genome differential_expression/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
--ref_annotation differential_expression/Homo_sapiens.GRCh38.109.gtf.gz \ --ref_annotation differential_expression/Homo_sapiens.GRCh38.109.gtf.gz \
--direct_rna --ref_transcriptome differential_expression/Homo_sapiens.GRCh38.cdna.all.fa.gz \ --direct_rna --ref_transcriptome differential_expression/Homo_sapiens.GRCh38.cdna.all.fa.gz \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
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,decompress_transcriptome,preprocess_ref_transcriptome build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "differential_expression_mouse" - if: $MATRIX_NAME == "differential_expression_mouse"
variables: variables:
NF_BEFORE_SCRIPT: wget -O differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf differential_expression_mouse.tar.gz NF_BEFORE_SCRIPT: wget -O differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf differential_expression_mouse.tar.gz && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \ NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression_mouse/differential_expression_fastq \ --fastq differential_expression_mouse/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome-source precomputed --de_analysis \
--ref_genome differential_expression_mouse/GRCm39.genome.fa.gz \ --ref_genome differential_expression_mouse/GRCm39.genome.fa.gz \
--ref_annotation differential_expression_mouse/gencode.vM33.annotation.gtf \ --ref_annotation differential_expression_mouse/gencode.vM33.annotation.gtf \
--direct_rna --ref_transcriptome differential_expression_mouse/gencode.vM33.transcripts.fa.gz \ --direct_rna --ref_transcriptome differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv \
-c demo.nextflow.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation, preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,
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

1
CHANGELOG.md
View File

@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Renamed files: - Renamed files:
- `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv` - `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv`
- `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv` - `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv`
- Minimum memory requirements to `32 GB`.
### Added ### Added
- Published isoforms table to output directory. - Published isoforms table to output directory.
- Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts. - Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts.

2
README.md
View File

@ -27,7 +27,7 @@ Recommended requirements:
Minimum requirements: Minimum requirements:
+ CPUs = 8 + CPUs = 8
+ Memory = 16GB + Memory = 32GB
Approximate run time: 15 minutes per sample, with 1 million reads and recommended resources. Approximate run time: 15 minutes per sample, with 1 million reads and recommended resources.

2
docs/03_compute_requirements.md
View File

@ -6,7 +6,7 @@ Recommended requirements:
Minimum requirements: Minimum requirements:
+ CPUs = 8 + CPUs = 8
+ Memory = 16GB + Memory = 32GB
Approximate run time: 15 minutes per sample, with 1 million reads and recommended resources. Approximate run time: 15 minutes per sample, with 1 million reads and recommended resources.

18
main.nf
View File

@ -19,7 +19,7 @@ OPTIONAL_FILE = file("$projectDir/data/OPTIONAL_FILE")
process getVersions { process getVersions {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
output: output:
path "versions.txt" path "versions.txt"
script: script:
@ -44,7 +44,7 @@ process getVersions {
process getParams { process getParams {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
output: output:
path "params.json" path "params.json"
script: script:
@ -60,7 +60,7 @@ process getParams {
process decompress_ref { process decompress_ref {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
input: input:
path compressed_ref path compressed_ref
output: output:
@ -74,7 +74,7 @@ process decompress_ref {
process decompress_annotation { process decompress_annotation {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
input: input:
path compressed_annotation path compressed_annotation
output: output:
@ -89,7 +89,7 @@ process decompress_annotation {
process decompress_transcriptome { process decompress_transcriptome {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
input: input:
path "compressed_ref.gz" path "compressed_ref.gz"
output: output:
@ -104,7 +104,7 @@ process decompress_transcriptome {
process preprocess_ref_annotation { process preprocess_ref_annotation {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
input: input:
path ref_annotation path ref_annotation
output: output:
@ -119,7 +119,7 @@ process preprocess_ref_annotation {
process preprocess_ref_transcriptome { process preprocess_ref_transcriptome {
label "isoforms" label "isoforms"
cpus 1 cpus 1
memory "500MB" memory "2 GB"
input: input:
path "ref_transcriptome" path "ref_transcriptome"
output: output:
@ -177,7 +177,7 @@ process build_minimap_index{
*/ */
label "isoforms" label "isoforms"
cpus params.threads cpus params.threads
memory "16 GB" memory "31 GB"
input: input:
path reference path reference
@ -367,7 +367,7 @@ process merge_transcriptomes {
// Merge the transcriptomes from all samples // Merge the transcriptomes from all samples
label 'isoforms' label 'isoforms'
cpus 2 cpus 2
memory "4 GB" memory "2 GB"
input: input:
path "query_annotations/*" path "query_annotations/*"
path ref_annotation path ref_annotation

2
nextflow_schema.json
View File

@ -388,7 +388,7 @@
}, },
"minimum": { "minimum": {
"cpus": 8, "cpus": 8,
"memory": "16GB" "memory": "32GB"
}, },
"run_time": "15 minutes per sample, with 1 million reads and recommended resources.", "run_time": "15 minutes per sample, with 1 million reads and recommended resources.",
"arm_support": false "arm_support": false

2
subworkflows/reference_assembly.nf
View File

@ -6,7 +6,7 @@ process map_reads{
*/ */
label "isoforms" label "isoforms"
cpus params.threads cpus params.threads
memory "16 GB" memory "31 GB"
input: input:
tuple val(sample_id), path (fastq_reads), path(index), path(reference) tuple val(sample_id), path (fastq_reads), path(index), path(reference)