Access to undefined channel output bug CW-5398
This commit is contained in:
Neil Horner
parent
4c46f88f00
commit
c8c5922965
@ -7,7 +7,7 @@ variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
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--de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
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--transcriptome-source ${CI_PROJECT_NAME}/data/reference-guided \
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--transcriptome_source reference-guided \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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@ -66,21 +66,21 @@ docker-run:
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- if: $MATRIX_NAME == "isoforms"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
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--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 \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "isoforms_bam"
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variables:
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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
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NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome-source reference-guided \
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NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome_source reference-guided \
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--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 \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "no_ref_annotation"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
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--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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NF_IGNORE_PROCESSES: run_gffcompare,check_annotation_strand,preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
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@ -89,7 +89,7 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
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--de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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@ -98,7 +98,7 @@ docker-run:
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
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--transcriptome-source precomputed \
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--transcriptome_source precomputed \
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--de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff \
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@ -107,13 +107,13 @@ docker-run:
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--sample_sheet test_data/sample_sheet.csv \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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preprocess_reads,faidx,gz_faidx,merge_transcriptomes,merge_gff_bundles,assemble_transcripts,decompress_annotation,decompress_ref,
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build_minimap_index,get_transcriptome,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "differential_expression_gff3"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
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--transcriptome-source precomputed \
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--transcriptome_source precomputed \
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--de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff3 \
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@ -129,7 +129,6 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
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--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
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--transcriptome-source precomputed \
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--de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
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@ -144,7 +143,7 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
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--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
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--transcriptome-source precomputed --de_analysis \
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--transcriptome_source precomputed --de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
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--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
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@ -172,7 +171,7 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
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--fastq ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \
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--transcriptome-source precomputed --de_analysis \
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--transcriptome_source precomputed --de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_mouse/GRCm39.genome.fa.gz \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.annotation.gtf \
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--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
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@ -186,7 +185,7 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
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--de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/unstranded_annotation.gtf \
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--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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@ -213,7 +212,7 @@ docker-run:
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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
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NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
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--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
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--transcriptome-source precomputed --de_analysis \
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--transcriptome_source precomputed --de_analysis \
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--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
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--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
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--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
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@ -222,5 +221,5 @@ docker-run:
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-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome,faidx,gz_faidx
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@ -5,8 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Fixed
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- Bug that led to incorrect gene_id being assigned in the DE plots.
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- Fix v1.4.0 bug; access to undefined channel output bug when using precomputed transcriptome.
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## [v1.5.0]
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### Updated
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@ -250,7 +250,7 @@ def transcriptome_summary(report, summaries_dir):
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tabs = Tabs()
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data = {}
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# Load all the dataframes upfront to get sample_id for sorting.
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for summ_file in summaries_dir.glob('summary_*.tsv'):
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for summ_file in summaries_dir.glob('summary_*.pkl'):
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with open(summ_file, 'rb') as fh:
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summ = pickle.load(fh)
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sample_id = summ['sample_id']
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11
main.nf
11
main.nf
@ -404,7 +404,7 @@ process makeReport {
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path gff_annotation, stageAs: "gff_annotation/*"
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path de_report, stageAs: "de_report/*"
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path isoforms_table, stageAs: "isoforms_table/*"
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path "transcriptome_summary/summary_*.tsv"
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path transcriptome_summary, stageAs: "transcriptome_summary/summary_*.pkl"
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output:
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path ("wf-transcriptomes-*.html"), emit: report
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@ -422,6 +422,7 @@ process makeReport {
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String aln_stats_opts = aln_stats.fileName.name == OPTIONAL_FILE.name ? "" : "--alignment_stats aln_stats/"
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String pychop_opts = pychopper.fileName.name == OPTIONAL_FILE.name ? "" : "--pychop_report pychopper_report/"
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String iso_table_opts = isoforms_table.fileName.name == OPTIONAL_FILE.name ? "" : "--isoform_table isoforms_table/"
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String tr_summary_opts = transcriptome_summary.fileName.name == OPTIONAL_FILE.name ? "" : "--transcriptome_summary transcriptome_summary/"
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"""
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echo '${metadata}' > metadata.json
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workflow-glue report \
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@ -438,7 +439,7 @@ process makeReport {
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$gffcmp_opts \
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--isoform_table_nrows ${params.isoform_table_nrows} \
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$de_report_opts \
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--transcriptome_summary transcriptome_summary/
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$tr_summary_opts
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"""
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}
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@ -633,6 +634,7 @@ workflow pipeline {
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full_len_reads = input_reads.map{ meta, reads -> [meta.alias, reads]}
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pychopper_report = OPTIONAL_FILE
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}
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if (params.transcriptome_source != "precomputed"){
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build_minimap_index(ref_genome)
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log.info("Doing reference based transcript analysis")
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@ -645,6 +647,8 @@ workflow pipeline {
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assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann)
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merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple())
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transcriptome_summary = merge_gff_bundles.out.summary.map {it[1]}.collect()
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// only run gffcompare if ref annotation provided. Otherwise create optional files and channels
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if (params.ref_annotation){
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run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
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@ -679,6 +683,7 @@ workflow pipeline {
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isoforms_table = OPTIONAL_FILE
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merge_gff = OPTIONAL_FILE
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assembly_stats = OPTIONAL_FILE
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transcriptome_summary = OPTIONAL_FILE
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use_ref_ann = false
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}
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if (params.de_analysis){
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@ -732,7 +737,7 @@ workflow pipeline {
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merge_gff,
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de_report,
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isoforms_table,
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merge_gff_bundles.out.summary.map {it[1]}.collect())
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transcriptome_summary)
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report = makeReport.out.report
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