Feature/restructure outputs #6
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KateSakharova
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mberacochea
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May 29, 2024
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Thanks Kate. I left you some comments.
One thing that is missing is the study / run version on the folder name
SRPXXX / SRPXXXX
├── SRR1240
│ ├── SRR12403548
│ │ │ ├── assembly
│ │ │ ├── decontamination
│ │ │ │ └── SRR6180434.txt
│ │ │ ├── spades
│ │ │ │ └── 3.15.5
│ │ │ │ ├── params.txt
│ │ │ │ ├── SRR6180434.assembly_graph.fastg.gz
│ │ │ │ ├── SRR6180434.assembly_graph_with_scaffolds.gfa.gz
│ │ │ │ ├── SRR6180434.contigs.fa.gz
│ │ │ │ └── SRR6180434.scaffolds.fa.gz
| | | | └── coverage
│ │ │ │ └── SRR6180434.txt.gz
| | | | └── qc
│ │ │ | ├── multiqc
│ │ │ | │ ├── multiqc_data
│ │ │ | │ ├── multiqc_plots
│ │ │ | │ └── multiqc_report.html
│ │ │ | └── quast
│ │ │ | ├── SRR6180434
│ │ │ | └── versions.yml
│ │ ├── pipeline_info
│ │ │ ├── execution_report_2024-05-17_16-17-51.html
│ │ │ ├── execution_timeline_2024-05-17_16-17-51.html
│ │ │ ├── execution_trace_2024-05-17_16-17-51.txt
│ │ │ ├── params_2024-05-17_16-18-58.json
│ │ │ ├── pipeline_dag_2024-05-17_16-17-51.html
│ │ │ └── software_versions.yml
│ │ └── qc
│ │ ├── fastp
│ │ │ ├── SRR6180434.fastp.html
│ │ │ ├── SRR6180434.fastp.json
│ | │ └── SRR6180434.fastp.log
│ │ └── fastqc
│ | ├── decontaminated_SRR6180434_1_fastqc.html
│ │ ├── decontaminated_SRR6180434_1_fastqc.zip
│ │ ├── decontaminated_SRR6180434_2_fastqc.html
│ │ ├── decontaminated_SRR6180434_2_fastqc.zip
│ │ ├── SRR6180434_1_fastqc.html
│ │ ├── SRR6180434_1_fastqc.zip
│ │ ├── SRR6180434_2_fastqc.html
│ │ ├── SRR6180434_2_fastqc.zip
│ │ └── versions.yml_fastqc.zip
│ │ └── versions.yml
The attached multiqc report looks very good, but it has an extra software section include only fastqc:
workflows/miassembler.nf
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| } | ||
| qc_reads_extended.branch { meta, reads -> | ||
| megahit: params.assembler == "megahit" | ||
| || meta.single_end == true |
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I think we can remove the or meta.single_end bits, that is already decided by now
| @@ -21,7 +21,7 @@ process SAMTOOLS_BAM2FQ { | |||
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| script: | |||
| def args = task.ext.args ?: '' | |||
| def prefix = task.ext.prefix ?: "${meta.id}" | |||
| def prefix = task.ext.prefix ? "decontaminated_${meta.id}": "${meta.id}" | |||
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To keep things consistent, I would put this one in the task.ext in the modules just like BWA_MEM2 (https://github.com/EBI-Metagenomics/miassembler/pull/6/files#diff-bf809c928cb10b54d251dec8a140a2d5505150f97175d8d7b51dda9cc57971feR88)
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We also need to remove any mentions about this workflow being part of nf-core, such as the multiqc methods text: |
KateSakharova
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Adjust the params in the nextflow.config to match the schema (they must match) Re-generated some modules patches
Rename decontaminated.txt.
…ts_mbc Some tweaks on top of the restructure_outputs branch.
mberacochea
approved these changes
May 30, 2024
I think this is ready to be merge now
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Updates:
I added FASTQC for decontaminated reads. Renamed files in decontamination step very urgly...
MultiQC report example. Have a look!
multiqc_report.html.zip
Current structure:
Problems:
I can output assembly into assembler/version, but I can't easily add coverage/qc/decontamination into that folder. For assembly process we do not refer to params.assembler because we have this lovely bit:
and if I use
$params.assembler / coverage(where requested assembler = spades) but during pipeline assembler was changed to megahit - then coverage would be inspadesbut assembly results would be inmegahit(because that process was launched).TODO: