Merge branch 'cw-7270-readme' into 'dev'

Update readme for alignment and ingress outputs [CW-7270]

See merge request epi2melabs/workflows/wf-transcriptomes!288

README.md

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

docs/06_pipeline_overview.md

@@ -21,8 +21,7 @@ The workflow's choice of SQANTI3 as a companion QC and annotation layer matches
 
 The shared EPI2ME input handling collects FASTQ or BAM inputs, works out
 whether you have a single sample or a multiplexed run, and produces per-sample
-FASTQ files plus read statistics. These files are published under
+FASTQ files plus read statistics. These files are used in the downstream report.
-`ingress_results/<alias>/` and are used in the downstream report.
 
 ### 2. Sample sheet formulation
 
@@ -65,7 +64,7 @@ requirements for a two-group DE/DTU comparison.
 Each sample is aligned to the supplied reference genome with
 [`minimap2`](https://github.com/lh3/minimap2), then sorted and indexed with
 [`samtools`](https://www.htslib.org/). The aligned BAMs under
-`cohort/alignments/` are the main alignment files used for transcriptome
+`samples/<alias>/alignment/` are the main alignment files used for transcriptome
 analysis, optional `SQANTI3` QC, and optional IGV viewing.
 
 ### 4. Cohort transcriptome construction
@@ -122,11 +121,8 @@ The workflow's analysis is controlled by a user provided genome, annotation, and
 The published outputs are organised around a small number of top-level
 directories:
 
-+ `ingress_results/<alias>/` contains prepared reads, read statistics, and sample
++ `cohort/` contains the primary joint `bambu` transcriptome, count tables, and optional cohort `SQANTI3` outputs
-  metadata for each sample
++ `samples/<alias>/` contains alignments, independent per-sample `bambu` outputs and
-+ `cohort/` contains the primary joint `bambu` transcriptome, count tables,
-  alignments, and optional cohort `SQANTI3` outputs
-+ `samples/<alias>/` contains the independent per-sample `bambu` outputs and
   optional per-sample `SQANTI3` outputs
 + `de_analysis/<contrast>/` contains DE and DTU results for each contrast when
   differential analysis is enabled

docs/08_outputs.md

@@ -3,10 +3,6 @@ Output files may be aggregated including information for all samples or provided
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|
 | Workflow report | wf-transcriptomes-report.html | HTML report summarising transcript discovery, quantification, optional SQANTI3 classification, and optional differential analysis results. | aggregated |
-| 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 |
-| 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 |
-| Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample |
-| Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample |
 | Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample |
 | Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
 | Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |

docs/10_troubleshooting.md

@@ -50,7 +50,7 @@ In the current version DE and DTU results are grouped by contrast under
 #### I expected the old output layout or transcriptome files
 
 The previous workflow version emitted one flat set of transcriptome.
-In the current versions, the output folder is organised around `ingress_results/`,
+In the current versions, the output folder is organised around
 `cohort/`, `samples/<alias>/`, `de_analysis/<contrast>/`, and
 `igv_reference/`.
 

output_definition.json

@@ -8,38 +8,6 @@
       "optional": false,
       "type": "aggregated"
     },
-    "read-stats-per-file": {
-      "filepath": "ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv",
-      "title": "Per-file read stats",
-      "description": "Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available.",
-      "mime-type": "text/tab-separated-values",
-      "optional": true,
-      "type": "per-sample"
-    },
-    "read-stats-per-read": {
-      "filepath": "ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz",
-      "title": "Per-read stats",
-      "description": "Read statistics for individual reads in a sample, when this output is enabled.",
-      "mime-type": "application/gzip",
-      "optional": true,
-      "type": "per-sample"
-    },
-    "sample-fastq": {
-      "filepath": "ingress_results/{{ alias }}/seqs.fastq.gz",
-      "title": "Ingress reads",
-      "description": "Reads prepared from the input data for downstream analysis.",
-      "mime-type": "application/gzip",
-      "optional": true,
-      "type": "per-sample"
-    },
-    "sample-metadata": {
-      "filepath": "ingress_results/{{ alias }}/metamap.json",
-      "title": "Ingress metadata",
-      "description": "Per-sample metadata used by the workflow.",
-      "mime-type": "application/json",
-      "optional": true,
-      "type": "per-sample"
-    },
     "sample-bam": {
       "filepath": "samples/{{ alias }}/alignment/reads.bam",
       "title": "Aligned BAM",