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BAM input CW-3512

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This commit is contained in:
Neil Horner 2024-06-04 09:25:31 +00:00
parent 7ca0d269f4
commit cfa41f16d0
7 changed files with 67 additions and 31 deletions
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9
.gitlab-ci.yml
View File

@ -50,7 +50,7 @@ docker-run:
parallel:
matrix:
- MATRIX_NAME: [
"fusions", "differential_expression", "isoforms",
"fusions", "differential_expression", "isoforms", "isoforms_bam",
"only_differential_expression", "differential_expression_gff3",
"ncbi_gzip", "ncbi_no_gene_id", "ensembl_with_versions",
"differential_expression_mouse", "no_ref_annotation"
@ -68,6 +68,13 @@ docker-run:
--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"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "isoforms_bam"
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_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 \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
- if: $MATRIX_NAME == "no_ref_annotation"
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

6
README.md
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@ -86,9 +86,9 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec
## Input example
<!---Example of input directory structure, delete and edit as appropriate per workflow.--->
This workflow accepts FASTQ files as input.
This workflow accepts either FASTQ or BAM files as input.
The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates).
The FASTQ or BAM input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ or BAM file; (ii) the path to a top-level directory containing FASTQ or BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ or BAM files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`.
```
(i) (ii) (iii)
@ -106,7 +106,6 @@ input_reads.fastq ─── input_directory ─── input_directory
## Input parameters
### Input Options
@ -114,6 +113,7 @@ input_reads.fastq ─── input_directory ─── input_directory
| Nextflow parameter name | Type | Description | Help | Default |
|--------------------------|------|-------------|------|---------|
| fastq | string | FASTQ files to use in the analysis. | This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. | |
| bam | string | BAM or unaligned BAM (uBAM) files to use in the analysis. | This accepts one of three cases: (i) the path to a single BAM file; (ii) the path to a top-level directory containing BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain BAM files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. | |
| transcriptome_source | string | Select how the transcriptome used for analysis should be prepared. | To analyse only gene fusions and differential expression use of an existing transcriptome may be preferred and so 'precomputed' should be selected. In this case the 'ref_transcriptome' parameter should be specified. To create a reference transcriptome using an existing reference genome, select 'reference guided' and specify the 'ref_genome' parameter. | reference-guided |
| ref_genome | string | Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow. | A reference genome is required for reference-based assembly of a transcriptome. | |
| ref_transcriptome | string | Transcriptome reference file. Required for precomputed transcriptome calculation and for differential expression analysis. | A reference transcriptome related to the sample under study. Must be supplied when the 'Transcriptome source' parameter has been set to 'precomputed' or to perform differential expression. | |

6
docs/06_input_example.md
View File

@ -1,7 +1,7 @@
<!---Example of input directory structure, delete and edit as appropriate per workflow.--->
This workflow accepts FASTQ files as input.
This workflow accepts either FASTQ or BAM files as input.
The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates).
The FASTQ or BAM input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ or BAM file; (ii) the path to a top-level directory containing FASTQ or BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ or BAM files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`.
```
(i) (ii) (iii)
@ -15,4 +15,4 @@ input_reads.fastq ─── input_directory ─── input_directory
│ └── reads2.fastq
└── barcode03
└── reads0.fastq
```
```

1
docs/06_input_parameters.md
View File

@ -3,6 +3,7 @@
| Nextflow parameter name | Type | Description | Help | Default |
|--------------------------|------|-------------|------|---------|
| fastq | string | FASTQ files to use in the analysis. | This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. | |
| bam | string | BAM or unaligned BAM (uBAM) files to use in the analysis. | This accepts one of three cases: (i) the path to a single BAM file; (ii) the path to a top-level directory containing BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain BAM files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. | |
| transcriptome_source | string | Select how the transcriptome used for analysis should be prepared. | To analyse only gene fusions and differential expression use of an existing transcriptome may be preferred and so 'precomputed' should be selected. In this case the 'ref_transcriptome' parameter should be specified. To create a reference transcriptome using an existing reference genome, select 'reference guided' and specify the 'ref_genome' parameter. | reference-guided |
| ref_genome | string | Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow. | A reference genome is required for reference-based assembly of a transcriptome. | |
| ref_transcriptome | string | Transcriptome reference file. Required for precomputed transcriptome calculation and for differential expression analysis. | A reference transcriptome related to the sample under study. Must be supplied when the 'Transcriptome source' parameter has been set to 'precomputed' or to perform differential expression. | |

51
main.nf
View File

@ -9,7 +9,7 @@ import nextflow.util.BlankSeparatedList;
import java.util.ArrayList;
nextflow.enable.dsl = 2
include { fastq_ingress } from './lib/ingress'
include { fastq_ingress; xam_ingress } from './lib/ingress'
include { reference_assembly } from './subworkflows/reference_assembly'
include { gene_fusions } from './subworkflows/JAFFAL/gene_fusions'
include { differential_expression } from './subworkflows/differential_expression'
@ -737,18 +737,12 @@ workflow {
Pinguscript.ping_start(nextflow, workflow, params)
fastq = file(params.fastq, type: "file")
error = null
if (params.containsKey("minimap_index_opts")) {
error = "`--minimap_index_opts` parameter is deprecated. Use parameter `--minimap2_index_opts` instead."
}
if (!fastq.exists()) {
error = "--fastq: File doesn't exist, check path."
}
if (params.transcriptome_source == "precomputed" && !params.ref_transcriptome){
error = "As transcriptome source parameter is precomputed you must include a ref_transcriptome parameter"
}
@ -808,22 +802,35 @@ workflow {
}
if (error){
throw new Exception(error)
}else{
reads = samples = fastq_ingress([
"input":params.fastq,
"sample":params.sample,
"sample_sheet":params.sample_sheet,
"analyse_unclassified":params.analyse_unclassified,
"stats": true,
"fastcat_extra_args": "",
"per_read_stats": true])
pipeline(reads, ref_genome, ref_annotation,
jaffal_refBase, params.jaffal_genome, params.jaffal_annotation,
ref_transcriptome, use_ref_ann)
output(pipeline.out.results)
}
if (params.fastq) {
samples = fastq_ingress([
"input":params.fastq,
"sample":params.sample,
"sample_sheet":params.sample_sheet,
"analyse_unclassified":params.analyse_unclassified,
"stats": true,
"fastcat_extra_args": "",
"per_read_stats": true])
} else {
samples = xam_ingress([
"input":params.bam,
"sample":params.sample,
"sample_sheet":params.sample_sheet,
"analyse_unclassified":params.analyse_unclassified,
"keep_unaligned": true,
"return_fastq": true,
"stats": true,
"per_read_stats": true])
}
pipeline(samples, ref_genome, ref_annotation,
jaffal_refBase, params.jaffal_genome, params.jaffal_annotation,
ref_transcriptome, use_ref_ann)
output(pipeline.out.results)
}
workflow.onComplete {

1
nextflow.config
View File

@ -13,6 +13,7 @@
params {
help = false
fastq = null
bam = null
ref_genome = null
ref_annotation = null
transcriptome_source = "reference-guided"

24
nextflow_schema.json
View File

@ -23,6 +23,12 @@
"description": "FASTQ files to use in the analysis.",
"help_text": "This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`."
},
"bam": {
"type": "string",
"format": "path",
"description": "BAM or unaligned BAM (uBAM) files to use in the analysis.",
"help_text": "This accepts one of three cases: (i) the path to a single BAM file; (ii) the path to a top-level directory containing BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain BAM files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`."
},
"transcriptome_source": {
"type": "string",
"enum": [
@ -74,10 +80,24 @@
"allOf": [
{
"required": [
"fastq",
"transcriptome_source"
]
}]
},
{
"oneOf": [
{
"required": [
"fastq"
]
},
{
"required": [
"bam"
]
}
]
}
]
},
"output_options": {
"title": "Output Options",