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Access to undefined channel output bug CW-5398

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This commit is contained in:
Neil Horner 2024-12-13 11:51:04 +00:00
parent 4c46f88f00
commit c8c5922965
4 changed files with 24 additions and 21 deletions
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29
.gitlab-ci.yml
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@ -7,7 +7,7 @@ variables:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \ --de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
--transcriptome-source ${CI_PROJECT_NAME}/data/reference-guided \ --transcriptome_source reference-guided \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \ --direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
@ -66,21 +66,21 @@ docker-run:
- if: $MATRIX_NAME == "isoforms" - if: $MATRIX_NAME == "isoforms"
variables: variables:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \ --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "isoforms_bam" - if: $MATRIX_NAME == "isoforms_bam"
variables: variables:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome_source reference-guided \
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \ --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,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: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome-source reference-guided \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa \ --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_IGNORE_PROCESSES: run_gffcompare,check_annotation_strand,preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome NF_IGNORE_PROCESSES: run_gffcompare,check_annotation_strand,preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
@ -89,7 +89,7 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--de_analysis \ --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \ --direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
@ -98,7 +98,7 @@ docker-run:
variables: variables:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \ --transcriptome_source precomputed \
--de_analysis \ --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff \
@ -107,13 +107,13 @@ docker-run:
--sample_sheet test_data/sample_sheet.csv \ --sample_sheet test_data/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,faidx,gz_faidx,merge_transcriptomes,merge_gff_bundles,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,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: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \ --transcriptome_source precomputed \
--de_analysis \ --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff3 \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff3 \
@ -129,7 +129,6 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config 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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \ --fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \ --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
@ -144,7 +143,7 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config 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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \ --fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome_source precomputed --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \ --direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
@ -172,7 +171,7 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz -C ${CI_PROJECT_NAME}/data/&& wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz -C ${CI_PROJECT_NAME}/data/&& wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config 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 ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \ --fastq ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome_source precomputed --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_mouse/GRCm39.genome.fa.gz \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_mouse/GRCm39.genome.fa.gz \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.annotation.gtf \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.annotation.gtf \
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.transcripts.fa.gz \ --direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
@ -186,7 +185,7 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \ NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--de_analysis \ --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/unstranded_annotation.gtf \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/unstranded_annotation.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \ --direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
@ -213,7 +212,7 @@ docker-run:
NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression_ncbi.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression_ncbi.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config 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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \ --fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \ --transcriptome_source precomputed --de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \ --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \ --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \ --direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
@ -222,5 +221,5 @@ docker-run:
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config" -c ${CI_PROJECT_NAME}/data/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,faidx,gz_faidx

3
CHANGELOG.md
View File

@ -5,8 +5,7 @@ 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). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased] ## [Unreleased]
### Fixed - Fix v1.4.0 bug; access to undefined channel output bug when using precomputed transcriptome.
- Bug that led to incorrect gene_id being assigned in the DE plots.
## [v1.5.0] ## [v1.5.0]
### Updated ### Updated

2
bin/workflow_glue/report.py
View File

@ -250,7 +250,7 @@ def transcriptome_summary(report, summaries_dir):
tabs = Tabs() tabs = Tabs()
data = {} data = {}
# Load all the dataframes upfront to get sample_id for sorting. # Load all the dataframes upfront to get sample_id for sorting.
for summ_file in summaries_dir.glob('summary_*.tsv'): for summ_file in summaries_dir.glob('summary_*.pkl'):
with open(summ_file, 'rb') as fh: with open(summ_file, 'rb') as fh:
summ = pickle.load(fh) summ = pickle.load(fh)
sample_id = summ['sample_id'] sample_id = summ['sample_id']

11
main.nf
View File

@ -404,7 +404,7 @@ process makeReport {
path gff_annotation, stageAs: "gff_annotation/*" path gff_annotation, stageAs: "gff_annotation/*"
path de_report, stageAs: "de_report/*" path de_report, stageAs: "de_report/*"
path isoforms_table, stageAs: "isoforms_table/*" path isoforms_table, stageAs: "isoforms_table/*"
path "transcriptome_summary/summary_*.tsv" path transcriptome_summary, stageAs: "transcriptome_summary/summary_*.pkl"
output: output:
path ("wf-transcriptomes-*.html"), emit: report path ("wf-transcriptomes-*.html"), emit: report
@ -422,6 +422,7 @@ process makeReport {
String aln_stats_opts = aln_stats.fileName.name == OPTIONAL_FILE.name ? "" : "--alignment_stats aln_stats/" String aln_stats_opts = aln_stats.fileName.name == OPTIONAL_FILE.name ? "" : "--alignment_stats aln_stats/"
String pychop_opts = pychopper.fileName.name == OPTIONAL_FILE.name ? "" : "--pychop_report pychopper_report/" String pychop_opts = pychopper.fileName.name == OPTIONAL_FILE.name ? "" : "--pychop_report pychopper_report/"
String iso_table_opts = isoforms_table.fileName.name == OPTIONAL_FILE.name ? "" : "--isoform_table isoforms_table/" String iso_table_opts = isoforms_table.fileName.name == OPTIONAL_FILE.name ? "" : "--isoform_table isoforms_table/"
String tr_summary_opts = transcriptome_summary.fileName.name == OPTIONAL_FILE.name ? "" : "--transcriptome_summary transcriptome_summary/"
""" """
echo '${metadata}' > metadata.json echo '${metadata}' > metadata.json
workflow-glue report \ workflow-glue report \
@ -438,7 +439,7 @@ process makeReport {
$gffcmp_opts \ $gffcmp_opts \
--isoform_table_nrows ${params.isoform_table_nrows} \ --isoform_table_nrows ${params.isoform_table_nrows} \
$de_report_opts \ $de_report_opts \
--transcriptome_summary transcriptome_summary/ $tr_summary_opts
""" """
} }
@ -633,6 +634,7 @@ workflow pipeline {
full_len_reads = input_reads.map{ meta, reads -> [meta.alias, reads]} full_len_reads = input_reads.map{ meta, reads -> [meta.alias, reads]}
pychopper_report = OPTIONAL_FILE pychopper_report = OPTIONAL_FILE
} }
if (params.transcriptome_source != "precomputed"){ if (params.transcriptome_source != "precomputed"){
build_minimap_index(ref_genome) build_minimap_index(ref_genome)
log.info("Doing reference based transcript analysis") log.info("Doing reference based transcript analysis")
@ -645,6 +647,8 @@ workflow pipeline {
assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann) assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann)
merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple()) merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple())
transcriptome_summary = merge_gff_bundles.out.summary.map {it[1]}.collect()
// only run gffcompare if ref annotation provided. Otherwise create optional files and channels // only run gffcompare if ref annotation provided. Otherwise create optional files and channels
if (params.ref_annotation){ if (params.ref_annotation){
run_gffcompare(merge_gff_bundles.out.gff, ref_annotation) run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
@ -679,6 +683,7 @@ workflow pipeline {
isoforms_table = OPTIONAL_FILE isoforms_table = OPTIONAL_FILE
merge_gff = OPTIONAL_FILE merge_gff = OPTIONAL_FILE
assembly_stats = OPTIONAL_FILE assembly_stats = OPTIONAL_FILE
transcriptome_summary = OPTIONAL_FILE
use_ref_ann = false use_ref_ann = false
} }
if (params.de_analysis){ if (params.de_analysis){
@ -732,7 +737,7 @@ workflow pipeline {
merge_gff, merge_gff,
de_report, de_report,
isoforms_table, isoforms_table,
merge_gff_bundles.out.summary.map {it[1]}.collect()) transcriptome_summary)
report = makeReport.out.report report = makeReport.out.report