Add start from bam #193
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Add start from bam #193
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Open
Lucpen
added
enhancement
fellen31
reviewed
Jan 9, 2025
| @@ -58,6 +58,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d | |||
| #### Salmon | |||
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| [`Salmon`](https://salmon.readthedocs.io/en/latest/) quantifies reads. | |||
| Note that as Salmon has been setup to start from fastq files, it will not run if the pipeline starts from bam files. | |||
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I don't know Salmon very well. Would it make sense to convert bam to fastq in order to run Salmon when starting from BAM?
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Yes, it would, however, I think that this should not be done in this PR, perhaps on the next one.
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| def id = "${ids}".replace("[","").replace("]","").replace(",","") | ||
| def single_end = "${single_ends}".replace("[","").replace("]","").replace(",","") | ||
| def sex_drop = "${sex}".replace("[","").replace("]","").replace(",","").replace("1","M").replace("2","F").replace("0","NA").replace("other","NA") | ||
| def strandedness = "${strandednesses}".replace("[","").replace("]","").replace(",","") | ||
| def id = ids.join(' ') | ||
| def single_end = single_ends.join(' ') | ||
| def sex_drop = sex.collect { it.replace("1","M").replace("2","F").replace("0","NA").replace("other","NA") }.join(' ') | ||
| def strandedness = strandednesses.join(' ') |
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It is more concise, just to prettify
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Okay, so the .replace(...) are no longer necessary?
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| SINGLE_ENDS=(${single_end}) | ||
| BAMS=(${bam.join(' ')}) | ||
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| # Check if single_end values are provided | ||
| updated_single_ends=() | ||
| for ((i=0; i<\${#SINGLE_ENDS[@]}; i++)); do | ||
| if [[ "\${SINGLE_ENDS[i]}" == "null" ]]; then | ||
| result=\$(samtools view -c -f 1 "\${BAMS[i]}" | awk '{print \$1 == 0 ? "true" : "false"}') | ||
| updated_single_ends+=("\$result") | ||
| else | ||
| updated_single_ends+=("\${SINGLE_ENDS[i]}") | ||
| fi | ||
| done | ||
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| # Convert updated_single_ends array to space-separated string and save to file | ||
| echo "\${updated_single_ends[*]}" > updated_single_ends.txt | ||
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It's hard for me to understand what's happening here. Are you checking if there are any paired ends in the BAM-file and then printing a false or true? Is this information not already in the meta/single_end input to this process?
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It will be there if one starts from fastq, but it won't if you start from bam, that's why I added it. I am very open to any suggestion on how to make it more readable, because I totally agree 😄
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| ch_fastq_reads // channel: [optional] [ val(meta), [path(reads)] ] | ||
| ch_bam_bai_reads // channel: [optional] [ val(meta), [path(bam) path(bai)] ] |
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Suggested change
| ch_fastq_reads // channel: [optional] [ val(meta), [path(reads)] ] | |
| ch_bam_bai_reads // channel: [optional] [ val(meta), [path(bam) path(bai)] ] | |
| ch_fastq_reads // channel: [optional] [ val(meta), [path(reads)] ] | |
| ch_bam_bai_reads // channel: [optional] [ val(meta), [path(bam) path(bai)] ] |
| ch_bam_reads = ch_bam_bai_reads.map { meta, bambai -> [ meta, bambai[0] ] } | ||
| ch_bai_reads = ch_bam_bai_reads.map { meta, bambai -> [ meta, bambai[1] ] } | ||
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| ch_bam_aligned=ch_bam_reads.mix(STAR_ALIGN.out.bam_sorted_aligned) |
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Suggested change
| ch_bam_aligned=ch_bam_reads.mix(STAR_ALIGN.out.bam_sorted_aligned) | |
| ch_bam_aligned = ch_bam_reads.mix(STAR_ALIGN.out.bam_sorted_aligned) |
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There can now also be aligned reads in ch_bam_reads right? ch_bam_aligned and ch_bai are "equivalents"?
I think I follow, but perhaps there could be more expressive names. It's a bit hard for me to see the difference between ch_bam_aligned + ch_bai, ch_bam_bai and ch_bam_bai_out together with the different ifs.
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| ch_samplesheet | ||
| .map { meta, files -> | ||
| [meta.sample, groupKey(meta + [id: meta.sample], meta.fq_pairs ?: 1), files] |
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How does meta.fq_pairs ?: 1 work for the bam branch?
| versions = ch_versions | ||
| emit: | ||
| samplesheet = ch_samplesheet | ||
| versions = ch_versions |
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Indent everything (from line 75 to here)?
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| def expectedNumber = meta[0].single_end ? 1 : 2 | ||
| def sampleNumber = files.flatten().size() | ||
| if (expectedNumber != sampleNumber) { | ||
| error("Samplesheet contains incorrect number of fastq files for sample ${sample}. Expected ${expectedNumber}, got ${sampleNumber}.") |
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| | `bam` | Full path to BAM file. | Provide either fastq_1 or bam | | ||
| | `bai` | Full path to BAM index file. | Provide either fastq_2 or bai | |
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Do the descriptions match here? "Provide either fastq_2 or bai"
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That part is whether the file is mandatory or not, its the third column
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I thought it was a copy paste error. Should bai not always be mandatory when you have bam then, or will it work without bai?
| @@ -98,17 +98,19 @@ Running the pipeline involves three steps: | |||
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| #### Samplesheet | |||
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| A samplesheet is used to pass the information about the sample(s), such as the path to the FASTQ files and other meta data (sex, phenotype, etc.,) to the pipeline in csv format. | |||
| A samplesheet is used to pass the information about the sample(s), such as the path to the FASTQ/BAM files and other meta data (sex, phenotype, etc.,) to the pipeline in csv format. | |||
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In long read unaligned reads are often stored as BAM files rather than fastq. Is it necessary to specify aligned reads for BAM, or would it be obvious to the user that BAM equals aligned reads?
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I am unsure to be honest, I even wonder if it would work uBAM
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I guess for most people BAM = aligned reads, so I think you can ignore my question.
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).