Fgumi initial commit

[freerkvandijk]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[matthdsm]

See comments

[matthdsm]

More being difficult

[matthdsm]

Still need to fix the tests

[freerkvandijk]

flowchart TD
    A["Input channel: meta + reads + aligner + index + fasta + gtf"] --> B{sample_type}
    B -->|RNA| R1[FASTQ_ALIGN_RNA]
    B -->|DNA| C{"meta.fgumi_aware == true"}

    C -->|false| D1["FASTQ_ALIGN_DNA non-UMI"]
    C -->|true| U0[Enter UMI_CONSENSUS_FGUMI]

    subgraph UMI_CONSENSUS_FGUMI
      U1["Step 1: FGUMI_EXTRACT<br/>reads -> unmapped BAM with UMI tags"]
      U1J["Join with reference assets<br/>SNAP index + fasta + dict from meta.genome_data"]
      U2["Step 3: FGUMI_SNAP_ZIPPER_SORT"]
      U2a["samtools sort -n<br/>unmapped BAM"]
      U2b[fgumi fastq]
      U2c[snap-aligner paired]
      U2d["samtools sort -n<br/>post-SNAP"]
      U2e[fgumi zipper]
      U2f["fgumi sort --order template-coordinate"]
      U3["Step 4: FGUMI_GROUP"]
      U4["Step 5: FGUMI_SIMPLEX"]
      U5J["Join simplex BAM with fasta"]
      U5["Step 7a: FGUMI_FILTER"]
      U6["Step 7b: FGUMI_SORT<br/>coordinate sort + index"]

      U1 --> U1J --> U2
      U2 --> U2a --> U2b --> U2c --> U2d --> U2e --> U2f
      U2f --> U3 --> U4 --> U5J --> U5 --> U6
    end

    D1 --> M1["Markdup branch selector<br/>bamsormadup | samtools | sort"]
    R1 --> M1

    U6 --> MIX1[Mix UMI BAM/BAI into common postprocess stream]
    U3 --> MET1[grouping_metrics]
    U3 --> MET2[family_size_histogram]
    U4 --> MET3[consensus_metrics]
    U5 --> MET4[filtering_metrics]
    U6 --> MET5[filtered_consensus_bam]

    M1 --> P1["BIOBAMBAM_BAMSORMADUP or SAMTOOLS_SORMADUP or SAMTOOLS_SORT"]
    P1 --> COMP{bam or cram}
    MIX1 --> COMP

    COMP -->|bam| CVT[SAMTOOLS_CONVERT to CRAM]
    COMP -->|cram| OUT1["cram + crai"]
    CVT --> OUT1

    OUT1 --> E1["emit: cram_crai"]
    MET1 --> E2["emit: sormadup_metrics"]
    MET2["emit: family_size_histogram"] --> E3
    MET5 --> E4["emit: filtered_consensus_bam"]

Loading

[matthdsm]

comments:

• why the name sort before alignment?
• figure out why the snap native name sort is insufficient for zipper
• replace 7b fgumi sort with samtools sort to enable direct to cram sorting

[matthdsm]

make sure all the RG info is encoded in the uBam so we don't lose any info