template update

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         always_run: true
         pass_filenames: false
         additional_dependencies:
-          - epi2melabs>=0.0.49
+          - epi2melabs>=0.0.50
       - id: build_models
         name: build_models
         entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py

CHANGELOG.md

@@ -4,10 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v1.0.0]
 ### Added
 - Published minimap2 and pychopper results to output directory.
 - Two extra pychopper parameters `--cdna_kit` and `--pychopper_backend`. `--pychopper_options` is still available to define any other options.
+- Memory requirements for each process.
+### Changed
+- Documentation.
 
 ## [v0.4.2]
 ### Changed

README.md

@@ -163,13 +163,13 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec
 
 ## Outputs
 
-Outputs files may be aggregated including information for all             samples or provided per sample. Per sample files             will be prefixed with respective aliases and represented             below as {{ alias }}.
+Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
 
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|
 | workflow report | wf-transcriptomes-report.html | a HTML report document detailing the primary findings of the workflow | aggregated |
 | Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
-| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
+| Read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
 | Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
 | Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
 | Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
@@ -180,7 +180,7 @@ Outputs files may be aggregated including information for all             sample
 | Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions . | aggregated |
 | Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
 | Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
-| Differential gene expression report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
+| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
 | Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
 | Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv  | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
 | Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |

docs/07_outputs.md

@@ -1,10 +1,10 @@
-Outputs files may be aggregated including information for all             samples or provided per sample. Per sample files             will be prefixed with respective aliases and represented             below as {{ alias }}.
+Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
 
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|
 | workflow report | wf-transcriptomes-report.html | a HTML report document detailing the primary findings of the workflow | aggregated |
 | Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
-| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
+| Read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
 | Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
 | Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
 | Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
@@ -15,7 +15,7 @@ Outputs files may be aggregated including information for all             sample
 | Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions . | aggregated |
 | Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
 | Differential transcript usage gene TSV | /de_analysis/results_dtu_gene.tsv | This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
-| Differential gene expression report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
+| Differential transcript usage report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
 | Differential transcript usage TSV | /de_analysis/results_dtu_transcript.tsv | This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression. | aggregated |
 | Differential transcript usage stageR TSV | /de_analysis/results_dtu_stageR.tsv  | This is the output from StageR and it shows both gene and transcript probabilities of differential expression | aggregated |
 | Differential transcript usage DEXSeq TSV | /de_analysis/results_dexseq.tsv | The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression. | aggregated |

lib/NfcoreSchema.groovy

@@ -141,7 +141,7 @@ class NfcoreSchema {
         for (specifiedParam in params.keySet()) {
             // nextflow params
             if (nf_params.contains(specifiedParam)) {
-                log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
+                log.error "You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
                 has_error = true
             }
             // unexpected params
@@ -180,7 +180,7 @@ class NfcoreSchema {
             schema.validate(params_json)
         } catch (ValidationException e) {
             println ''
-            log.error 'ERROR: Validation of pipeline parameters failed!'
+            log.error 'Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
             HashSet<String> observed_exceptions = []
             printExceptions(exceptionJSON, params_json, log, enums, raw_schema, observed_exceptions)

lib/ingress.nf

@@ -240,6 +240,7 @@ process checkBamHeaders {
     label "ingress"
     label "wf_common"
     cpus 1
+    memory "2 GB"
     input: tuple val(meta), path("input_dir/reads*.bam")
     output:
         // set the two env variables by `eval`-ing the output of the python script
@@ -257,6 +258,7 @@ process mergeBams {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input: tuple val(meta), path("input_bams/reads*.bam")
     output: tuple val(meta), path("reads.bam")
     shell:
@@ -271,6 +273,7 @@ process catSortBams {
     label "ingress"
     label "wf_common"
     cpus 4
+    memory "4 GB"
     input: tuple val(meta), path("input_bams/reads*.bam")
     output: tuple val(meta), path("reads.bam")
     script:
@@ -285,6 +288,7 @@ process sortBam {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input: tuple val(meta), path("reads.bam")
     output: tuple val(meta), path("reads.sorted.bam")
     script:
@@ -298,6 +302,7 @@ process bamstats {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "4 GB"
     input:
         tuple val(meta), path("reads.bam")
     output:
@@ -414,6 +419,7 @@ process move_or_compress_fq_file {
     label "ingress"
     label "wf_common"
     cpus 1
+    memory "2 GB"
     input:
         // don't stage `input` with a literal because we check the file extension
         tuple val(meta), path(input)
@@ -439,6 +445,7 @@ process fastcat {
     label "ingress"
     label "wf_common"
     cpus 3
+    memory "2 GB"
     input:
         tuple val(meta), path("input")
         val extra_args
@@ -737,6 +744,7 @@ process validate_sample_sheet {
     cpus 1
     label "ingress"
     label "wf_common"
+    memory "2 GB"
     input:
         path "sample_sheet.csv"
         val required_sample_types

nextflow.config

@@ -92,12 +92,12 @@ params {
 
     wf {
       example_cmd = [
-          "--fastq  'differential_expression/differential_expression_fastq'",
+        "--condition_sheet 'wf-transcriptomes-demo/condition_sheet.tsv'",
-          "--de_analysis --ref_genome 'differential_expression/hg38_chr20.fa'" ,
+        "--direct_rna",
-          "--transcriptome-source 'reference-guided'",
+        "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
-          "--ref_annotation 'differential_expression/gencode.v22.annotation.chr20.gtf'",
+        "--minimap2_index_opts '-k15'",
-          "--direct_rna --minimap2_index_opts '-k 15'  --sample_sheet 'differential_expression/sample_sheet.csv'",
+        "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
-          "--jaffal_refBase 'differential_expression/chr20/' --jaffal_genome 'hg38_chr20' --jaffal_annotation 'genCode22'"
+        "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"
@@ -112,7 +112,7 @@ manifest {
     description     = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.4.2'
+    version         = 'v1.0.0'
 }
 
 epi2melabs {

output_definition.json

@@ -18,7 +18,7 @@
     },
     "read-stats-per-read": {
       "filepath": "fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv",
-      "title": "Per file read stats",
+      "title": "Read stats",
       "description": "A TSV with per read stats, including all samples.",
       "mime-type": "text/tab-separated-values",
       "optional": false,
@@ -106,7 +106,7 @@
     },
     "dtu-report-pdf": {
       "filepath": "/de_analysis/results_dtu.pdf",
-      "title": "Differential gene expression report",
+      "title": "Differential transcript usage report",
       "description": "Summary report of differential transcript usage results as a PDF.",
       "mime-type": "application/pdf",
       "optional": true,
@@ -194,4 +194,4 @@
     }
    
   }
-}
+}