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Merge branch 'CW-2965' into 'dev'

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Error message if ref_genome and ref_annotation mismatch CW-2965

Closes CW-2965

See merge request epi2melabs/workflows/wf-transcriptomes!202
This commit is contained in:
Sarah Griffiths 2025-03-14 19:06:47 +00:00
commit 9900143122
3 changed files with 100 additions and 12 deletions
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58
.gitlab-ci.yml
View File

@ -55,7 +55,8 @@ docker-run:
"only_differential_expression", "differential_expression_gff3", "only_differential_expression", "differential_expression_gff3",
"ncbi_gzip", "ncbi_no_gene_id", "ensembl_with_versions", "ncbi_gzip", "ncbi_no_gene_id", "ensembl_with_versions",
"differential_expression_mouse", "no_ref_annotation", "differential_expression_mouse", "no_ref_annotation",
"unstranded_annotation_error", "igv", "igv_fai_gz" "unstranded_annotation_error", "igv", "igv_fai_gz",
"mismatch_seqid_error","mismatch_seqid_warn"
] ]
rules: rules:
# NOTE As we're overriding the rules block for the included docker-run # NOTE As we're overriding the rules block for the included docker-run
@ -69,21 +70,21 @@ docker-run:
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/mm2.config" -c ${CI_PROJECT_NAME}/data/mm2.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,validate_ref_annotation,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; ${MEM_CFG}" 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; ${MEM_CFG}"
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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.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,validate_ref_annotation,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; ${MEM_CFG}" 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; ${MEM_CFG}"
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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.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,validate_ref_annotation,check_annotation_strand,preprocess_reads,faidx,gz_faidx,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: "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; ${MEM_CFG}" 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; ${MEM_CFG}"
@ -107,7 +108,7 @@ 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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,merge_gff_bundles,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,faidx,validate_ref_annotation,gz_faidx,merge_transcriptomes,merge_gff_bundles,assemble_transcripts,decompress_annotation,decompress_ref,
build_minimap_index,get_transcriptome,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:
@ -122,7 +123,7 @@ 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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,validate_ref_annotation,faidx,gz_faidx,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:
@ -150,7 +151,7 @@ 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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts, preprocess_reads,faidx,validate_ref_annotation,gz_faidx,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:
@ -164,7 +165,7 @@ 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/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts, preprocess_reads,validate_ref_annotation,faidx,gz_faidx,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:
@ -178,7 +179,7 @@ docker-run:
--sample_sheet ${CI_PROJECT_NAME}/data/differential_expression_mouse/sample_sheet.csv \ --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression_mouse/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation, preprocess_reads,validate_ref_annotation,faidx,gz_faidx,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
- if: $MATRIX_NAME == "unstranded_annotation_error" - if: $MATRIX_NAME == "unstranded_annotation_error"
variables: variables:
@ -206,7 +207,7 @@ docker-run:
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, preprocess_reads,gz_faidx,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,validate_ref_annotation,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "igv_fai_gz" - if: $MATRIX_NAME == "igv_fai_gz"
variables: variables:
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; ${MEM_CFG}" 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; ${MEM_CFG}"
@ -220,6 +221,39 @@ docker-run:
--igv \ --igv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config" -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: > NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts, preprocess_reads,validate_ref_annotation,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome,faidx,gz_faidx build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome,faidx,gz_faidx
- if: $MATRIX_NAME == "mismatch_seqid_error"
variables:
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; ${MEM_CFG}"
NF_WORKFLOW_OPTS:
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
--de_analysis \
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/hg38_chr20.fa \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
--direct_rna \
--sample_sheet test_data/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
ASSERT_NEXTFLOW_FAILURE: 1
ASSERT_NEXTFLOW_FAILURE_REXP: Seqid mismatch found between the provided ref_annotation
- if: $MATRIX_NAME == "mismatch_seqid_warn"
variables:
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; ${MEM_CFG}"
NF_WORKFLOW_OPTS:
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
--de_analysis \
--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 \
--direct_rna \
--sample_sheet test_data/sample_sheet.csv --minimap2_index_opts '-w 25' \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: >
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
AFTER_NEXTFLOW_CMD: "grep 'are only present in the reference genome' '.nextflow.log'"

1
CHANGELOG.md
View File

@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased. - `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased.
- Updated recommended memory requirement. - Updated recommended memory requirement.
- Updated project description. - Updated project description.
- A common user issue is providing a ref_annotation and ref_genome parameter that have mismatched reference IDs, which causes the DE_analysis to fail. The workflow will now do an upfront check and give an error message if no overlap is found or a warning if some IDs are present in one file but not in the other.
- Reconciled workflow with wf-template v5.5.0. - Reconciled workflow with wf-template v5.5.0.
### Fixed ### Fixed
- `all_gene_counts.tsv` contained the DE counts results. - `all_gene_counts.tsv` contained the DE counts results.

53
main.nf
View File

@ -69,6 +69,54 @@ process decompress_ref {
""" """
} }
process validate_ref_annotation {
label "isoforms"
cpus 1
memory "2 GB"
input:
path "annotation.gtf"
path "reference.fasta"
output:
stdout
// Checks for overlap between seq_id column in annotation gtf and fasta reference ID's
// If no overlap is found exit
// Partial overlap (eg. user supplies genes/contigs of interest in annotation but the genome sequence) - warning
script:
"""
grep -v '^#' annotation.gtf | cut -f1 | sort -u > seq_ids.txt
awk '/^>/ {print substr(\$1,2)}' reference.fasta | sort -u > ref_ids.txt
matches=\$(comm -12 seq_ids.txt ref_ids.txt)
only_in_annotation=\$(comm -23 seq_ids.txt ref_ids.txt)
only_in_reference=\$(comm -13 seq_ids.txt ref_ids.txt)
if [[ -z "\$matches" ]]; then
echo "
ERROR: Seqid mismatch found between the provided ref_annotation (GTF/GFF)
file and ref_genome (FASTA).
For the reference guided differential expression subworkflow they must overlap.
" >&2
echo "Annotation ID examples:"
head -n 5 seq_ids.txt
echo "Reference ID examples:"
head -n 5 ref_ids.txt
echo "We recommend getting both files from the same source.
eg. both from Ensembl or both from NCBI.
Alternatively provide a pre-computed transcriptome using the ref_transcriptome parameter
See the README for more details on which inputs are supported."
exit 78
fi
if [[ -n "\$only_in_annotation" ]]; then
echo "Warning: Some sequence IDs are only present in the reference annotation and not the
reference genome so will not be used in downstream analysis eg."
echo "\$only_in_annotation" | head -n 5
fi
if [[ -n "\$only_in_reference" ]]; then
echo "Warning: Some FASTA reference IDs are only present in the reference genome
and not the reference annotation so will not be used in downstream analysis eg."
echo "\$only_in_reference" | head -n 5
fi
"""
}
process decompress_annotation { process decompress_annotation {
label "isoforms" label "isoforms"
@ -695,6 +743,11 @@ workflow pipeline {
stdoutput stdoutput
} }
if (!params.ref_transcriptome){ if (!params.ref_transcriptome){
validate_ref_annotation(ref_annotation, ref_genome).map { stdoutput ->
if (stdoutput) {
log.warn(stdoutput)
}
}
merge_transcriptomes(run_gffcompare.output.gtf.collect(), ref_annotation, ref_genome) merge_transcriptomes(run_gffcompare.output.gtf.collect(), ref_annotation, ref_genome)
transcriptome = merge_transcriptomes.out.fasta transcriptome = merge_transcriptomes.out.fasta
gtf = merge_transcriptomes.out.gtf gtf = merge_transcriptomes.out.gtf