Update readme for alignment and ingress outputs [CW-7270]
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Kiah McIntosh
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README.md
18
README.md
@ -176,8 +176,7 @@ The workflow's choice of SQANTI3 as a companion QC and annotation layer matches
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The shared EPI2ME input handling collects FASTQ or BAM inputs, works out
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whether you have a single sample or a multiplexed run, and produces per-sample
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FASTQ files plus read statistics. These files are published under
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`ingress_results/<alias>/` and are used in the downstream report.
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FASTQ files plus read statistics. These files are used in the downstream report.
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### 2. Sample sheet formulation
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@ -220,7 +219,7 @@ requirements for a two-group DE/DTU comparison.
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Each sample is aligned to the supplied reference genome with
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[`minimap2`](https://github.com/lh3/minimap2), then sorted and indexed with
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[`samtools`](https://www.htslib.org/). The aligned BAMs under
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`cohort/alignments/` are the main alignment files used for transcriptome
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`samples/<alias>/alignment/` are the main alignment files used for transcriptome
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analysis, optional `SQANTI3` QC, and optional IGV viewing.
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### 4. Cohort transcriptome construction
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@ -277,11 +276,8 @@ The workflow's analysis is controlled by a user provided genome, annotation, and
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The published outputs are organised around a small number of top-level
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directories:
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+ `ingress_results/<alias>/` contains prepared reads, read statistics, and sample
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metadata for each sample
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+ `cohort/` contains the primary joint `bambu` transcriptome, count tables,
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alignments, and optional cohort `SQANTI3` outputs
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+ `samples/<alias>/` contains the independent per-sample `bambu` outputs and
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+ `cohort/` contains the primary joint `bambu` transcriptome, count tables, and optional cohort `SQANTI3` outputs
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+ `samples/<alias>/` contains alignments, independent per-sample `bambu` outputs and
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optional per-sample `SQANTI3` outputs
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+ `de_analysis/<contrast>/` contains DE and DTU results for each contrast when
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differential analysis is enabled
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@ -362,10 +358,6 @@ Output files may be aggregated including information for all samples or provided
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| Title | File path | Description | Per sample or aggregated |
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|-------|-----------|-------------|--------------------------|
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| Workflow report | wf-transcriptomes-report.html | HTML report summarising transcript discovery, quantification, optional SQANTI3 classification, and optional differential analysis results. | aggregated |
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| Per-file read stats | ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv | Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available. | per-sample |
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| Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample |
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| Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample |
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| Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample |
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| Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample |
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| Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
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| Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |
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@ -466,7 +458,7 @@ In the current version DE and DTU results are grouped by contrast under
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#### I expected the old output layout or transcriptome files
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The previous workflow version emitted one flat set of transcriptome.
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In the current versions, the output folder is organised around `ingress_results/`,
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In the current versions, the output folder is organised around
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`cohort/`, `samples/<alias>/`, `de_analysis/<contrast>/`, and
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`igv_reference/`.
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@ -21,8 +21,7 @@ The workflow's choice of SQANTI3 as a companion QC and annotation layer matches
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The shared EPI2ME input handling collects FASTQ or BAM inputs, works out
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whether you have a single sample or a multiplexed run, and produces per-sample
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FASTQ files plus read statistics. These files are published under
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`ingress_results/<alias>/` and are used in the downstream report.
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FASTQ files plus read statistics. These files are used in the downstream report.
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### 2. Sample sheet formulation
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@ -65,7 +64,7 @@ requirements for a two-group DE/DTU comparison.
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Each sample is aligned to the supplied reference genome with
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[`minimap2`](https://github.com/lh3/minimap2), then sorted and indexed with
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[`samtools`](https://www.htslib.org/). The aligned BAMs under
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`cohort/alignments/` are the main alignment files used for transcriptome
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`samples/<alias>/alignment/` are the main alignment files used for transcriptome
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analysis, optional `SQANTI3` QC, and optional IGV viewing.
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### 4. Cohort transcriptome construction
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@ -122,11 +121,8 @@ The workflow's analysis is controlled by a user provided genome, annotation, and
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The published outputs are organised around a small number of top-level
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directories:
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+ `ingress_results/<alias>/` contains prepared reads, read statistics, and sample
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metadata for each sample
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+ `cohort/` contains the primary joint `bambu` transcriptome, count tables,
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alignments, and optional cohort `SQANTI3` outputs
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+ `samples/<alias>/` contains the independent per-sample `bambu` outputs and
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+ `cohort/` contains the primary joint `bambu` transcriptome, count tables, and optional cohort `SQANTI3` outputs
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+ `samples/<alias>/` contains alignments, independent per-sample `bambu` outputs and
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optional per-sample `SQANTI3` outputs
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+ `de_analysis/<contrast>/` contains DE and DTU results for each contrast when
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differential analysis is enabled
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@ -3,10 +3,6 @@ Output files may be aggregated including information for all samples or provided
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| Title | File path | Description | Per sample or aggregated |
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|-------|-----------|-------------|--------------------------|
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| Workflow report | wf-transcriptomes-report.html | HTML report summarising transcript discovery, quantification, optional SQANTI3 classification, and optional differential analysis results. | aggregated |
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| Per-file read stats | ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv | Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available. | per-sample |
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| Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample |
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| Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample |
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| Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample |
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| Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample |
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| Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
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| Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |
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@ -50,7 +50,7 @@ In the current version DE and DTU results are grouped by contrast under
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#### I expected the old output layout or transcriptome files
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The previous workflow version emitted one flat set of transcriptome.
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In the current versions, the output folder is organised around `ingress_results/`,
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In the current versions, the output folder is organised around
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`cohort/`, `samples/<alias>/`, `de_analysis/<contrast>/`, and
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`igv_reference/`.
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@ -8,38 +8,6 @@
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"optional": false,
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"type": "aggregated"
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},
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"read-stats-per-file": {
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"filepath": "ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv",
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"title": "Per-file read stats",
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"description": "Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "per-sample"
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},
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"read-stats-per-read": {
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"filepath": "ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz",
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"title": "Per-read stats",
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"description": "Read statistics for individual reads in a sample, when this output is enabled.",
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"mime-type": "application/gzip",
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"optional": true,
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"type": "per-sample"
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},
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"sample-fastq": {
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"filepath": "ingress_results/{{ alias }}/seqs.fastq.gz",
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"title": "Ingress reads",
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"description": "Reads prepared from the input data for downstream analysis.",
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"mime-type": "application/gzip",
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"optional": true,
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"type": "per-sample"
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},
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"sample-metadata": {
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"filepath": "ingress_results/{{ alias }}/metamap.json",
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"title": "Ingress metadata",
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"description": "Per-sample metadata used by the workflow.",
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"mime-type": "application/json",
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"optional": true,
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"type": "per-sample"
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},
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"sample-bam": {
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"filepath": "samples/{{ alias }}/alignment/reads.bam",
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"title": "Aligned BAM",
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