From d2ff47e882f580cdbccd6a18b53bfa66d50b9f3e Mon Sep 17 00:00:00 2001 From: liamlelievre Date: Thu, 5 Dec 2024 14:41:31 +1300 Subject: [PATCH] Run nf-test successfully in minimal and stub, renamed attr, updated docs --- docs/parameters.md | 142 ++++++++++++++++++++++++------------------- nextflow_schema.json | 12 ++-- 2 files changed, 84 insertions(+), 70 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index c9eaa7e..ef2bce2 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -4,19 +4,20 @@ A Nextflow pipeline for consensus, phased and pan-genome annotation. ## Input/output options -| Parameter | Description | Type | Default | Required | Hidden | -| ------------------------ | -------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ | -| `input` | Target assemblies listed in a CSV sheet | `string` | | True | | -| `protein_evidence` | Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file | `string` | | True | | -| `eggnogmapper_db_dir` | Eggnogmapper database directory | `string` | | | | -| `eggnogmapper_tax_scope` | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` | 1 | | - -| -| `rna_evidence` | FASTQ/BAM samples listed in a CSV sheet | `string` | | | | -| `liftoff_annotations` | Reference annotations listed in a CSV sheet | `string` | | | | -| `orthofinder_annotations` | Additional annotations for orthology listed in a CSV sheet | `string` | | | | -| `outdir` | The output directory where the results will be saved | `string` | | True | | -| `email` | Email address for completion summary. | `string` | | | True | +| Parameter | Description | Type | Default | Required | Hidden | +| ------------------------------------------ | ------------------------------------------------------------------------ | -------- | ------- | -------- | ------ | +| `input` | Target assemblies listed in a CSV sheet | `string` | | True | | +| `protein_evidence` | Protein evidence provided as a fasta file or multiple fasta files listed | +| in a plain txt file | `string` | | True | | +| `eggnogmapper_db_dir` | Eggnogmapper database directory | `string` | | | | +| `eggnogmapper_tax_scope` | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: | +| 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` | 1 | | | +| `rna_evidence` | FASTQ/BAM samples listed in a CSV sheet | `string` | | | | +| `liftoff_annotations` | Reference annotations listed in a CSV sheet | `string` | | | | +| `orthofinder_annotations` | Additional annotations for orthology listed in a CSV sheet | +| `string` | | | | +| `outdir` | The output directory where the results will be saved | `string` | | True | | +| `email` | Email address for completion summary. | `string` | | | True | ## Repeat annotation options @@ -29,68 +30,84 @@ A Nextflow pipeline for consensus, phased and pan-genome annotation. ## RNASeq pre-processing options -| Parameter | Description | Type | Default | Required | Hidden | -| ------------------------ | ------------------------------------------------------------------ | --------- | ----------------------------------------- | -------- | ------ | -| `fastqc_skip` | Skip FASTQC or not? | `boolean` | True | | | -| `fastp_skip` | Skip trimming by FASTQP or not? | `boolean` | | | | -| `min_trimmed_reads` | Exclude a sample if its reads after trimming are below this number | `integer` | 10000 | | | -| `fastp_extra_args` | Extra FASTP arguments | `string` | | | | -| `save_trimmed` | Save FASTQ files after trimming or not? | `boolean` | | | | -| `remove_ribo_rna` | Remove Ribosomal RNA or not? | `boolean` | | | | -| `save_non_ribo_reads` | Save FASTQ files after Ribosomal RNA removal or not? | `boolean` | | | | -| `ribo_database_manifest` | Ribosomal RNA fastas listed in a text sheet | `string` | ${projectDir}/assets/rrna-db-defaults.txt | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ----------------------------------------- | ------------------------------------------------------------------ | --------- | ------- | -------- | ------ | +| `fastqc_skip` | Skip FASTQC or not? | `boolean` | True | | | +| `fastp_skip` | Skip trimming by FASTQP or not? | `boolean` | | | | +| `min_trimmed_reads` | Exclude a sample if its reads after trimming are below this number | +| `integer` | 10000 | | | +| `fastp_extra_args` | Extra FASTP arguments | `string` | | | | +| `save_trimmed` | Save FASTQ files after trimming or not? | `boolean` | | | | +| `remove_ribo_rna` | Remove Ribosomal RNA or not? | `boolean` | | | | +| `save_non_ribo_reads` | Save FASTQ files after Ribosomal RNA removal or not? | `boolean` | | +| | +| `ribo_database_manifest` | Ribosomal RNA fastas listed in a text sheet | `string` | +| ${projectDir}/assets/rrna-db-defaults.txt | | | ## RNASeq alignment options -| Parameter | Description | Type | Default | Required | Hidden | -| ------------------------ | ------------------------------------------------- | --------- | ------- | -------- | ------ | -| `star_max_intron_length` | Maximum intron length for STAR alignment | `integer` | 16000 | | | -| `star_align_extra_args` | EXTRA arguments for STAR | `string` | | | | -| `star_save_outputs` | Save BAM files from STAR or not? | `boolean` | | | | -| `save_cat_bam` | SAVE a concatenated BAM file per assembly or not? | `boolean` | | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ------------------------ | ---------------------------------------- | --------- | ------- | -------- | ------ | +| `star_max_intron_length` | Maximum intron length for STAR alignment | `integer` | 16000 | | + +| +| `star_align_extra_args` | EXTRA arguments for STAR | `string` | | | | +| `star_save_outputs` | Save BAM files from STAR or not? | `boolean` | | | | +| `save_cat_bam` | SAVE a concatenated BAM file per assembly or not? | `boolean` | | | | ## Annotation options -| Parameter | Description | Type | Default | Required | Hidden | -| --------------------- | --------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ | -| `braker_extra_args` | Extra arguments for BRAKER | `string` | | | | -| `liftoff_coverage` | Liftoff coverage parameter | `number` | 0.9 | | | -| `liftoff_identity` | Liftoff identity parameter | `number` | 0.9 | | | -| `eggnogmapper_evalue` | Only report alignments below or equal the e-value threshold | `number` | 1e-05 | | | -| `eggnogmapper_pident` | Only report alignments above or equal to the given percentage of identity (0-100) | `integer` | 35 | | | +| Parameter | Description | Type | Default | Required | Hidden | +| --------------------- | ---------------------------------------------------------------- | -------- | ------- | -------- | ------ | +| `braker_extra_args` | Extra arguments for BRAKER | `string` | | | | +| `liftoff_coverage` | Liftoff coverage parameter | `number` | 0.9 | | | +| `liftoff_identity` | Liftoff identity parameter | `number` | 0.9 | | | +| `eggnogmapper_evalue` | Only report alignments below or equal the e-value threshold | `number` | +| 1e-05 | | | +| `eggnogmapper_pident` | Only report alignments above or equal to the given percentage of | +| identity (0-100) | `integer` | 35 | | | ## Post-annotation filtering options -| Parameter | Description | Type | Default | Required | Hidden | -| ----------------------------- | ----------------------------------------------------------------- | --------- | ------- | -------- | ------ | -| `allow_isoforms` | Allow multiple isoforms for gene models | `boolean` | True | | | -| `enforce_full_intron_support` | Require every model to have external evidence for all its introns | `boolean` | True | | | -| `filter_liftoff_by_hints` | Use BRAKER hints to filter Liftoff models | `boolean` | True | | | -| `eggnogmapper_purge_nohits` | Purge transcripts which do not have a hit against eggnog | `boolean` | | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ----------------------------- | --------------------------------------------------------- | --------- | ------- | -------- | ------ | +| `allow_isoforms` | Allow multiple isoforms for gene models | `boolean` | True | | | +| `enforce_full_intron_support` | Require every model to have external evidence for all its | +| introns | `boolean` | True | | | +| `filter_liftoff_by_hints` | Use BRAKER hints to filter Liftoff models | `boolean` | True | | + +| +| `eggnogmapper_purge_nohits` | Purge transcripts which do not have a hit against eggnog | +`boolean` | | | | ## Annotation output options -| Parameter | Description | Type | Default | Required | Hidden | -| --------------------- | ----------------- | --------- | ------- | -------- | ------ | -| `braker_save_outputs` | Save BRAKER files | `boolean` | | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ---------------------------------- | --------------------------------------------- | --------- | ------- | -------- | ------ | +| `braker_save_outputs` | Save BRAKER files | `boolean` | | | | +| `add_attrs_to_proteins_cds_fastas` | Add gff attributes to proteins/cDNA/cds fasta | `boolean` | +| | | | ## Evaluation options -| Parameter | Description | Type | Default | Required | Hidden | -| ------------------------ | --------------------------------------------------------------------------- | --------- | --------------- | -------- | ------ | -| `busco_skip` | Skip evaluation by BUSCO | `boolean` | | | | -| `busco_lineage_datasets` | BUSCO lineages as a space-separated list: 'fungi_odb10 microsporidia_odb10' | `string` | eukaryota_odb10 | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ------------------------ | ------------------------------------------------------ | --------------- | ------- | -------- | ------ | +| `busco_skip` | Skip evaluation by BUSCO | `boolean` | | | | +| `busco_lineage_datasets` | BUSCO lineages as a space-separated list: 'fungi_odb10 | +| microsporidia_odb10' | `string` | eukaryota_odb10 | | | ## Institutional config options Parameters used to describe centralised config profiles. These should not be edited. -| Parameter | Description | Type | Default | Required | Hidden | -| ---------------------------- | ----------------------------------------- | -------- | -------------------------------------------------------- | -------- | ------ | -| `custom_config_version` | Git commit id for Institutional configs. | `string` | master | | True | -| `custom_config_base` | Base directory for Institutional configs. | `string` | https://raw.githubusercontent.com/nf-core/configs/master | | True | -| `config_profile_name` | Institutional config name. | `string` | | | True | -| `config_profile_description` | Institutional config description. | `string` | | | True | +| Parameter | Description | Type | Default | Required | Hidden | +| -------------------------------------------------------- | ----------------------------------------- | -------- | ------- | -------- | ------ | +| `custom_config_version` | Git commit id for Institutional configs. | `string` | master | | +| True | +| `custom_config_base` | Base directory for Institutional configs. | `string` | +| https://raw.githubusercontent.com/nf-core/configs/master | | True | +| `config_profile_name` | Institutional config name. | `string` | | | True | +| `config_profile_description` | Institutional config description. | `string` | | | True | ## Generic options @@ -99,15 +116,12 @@ Less common options for the pipeline, typically set in a config file. | Parameter | Description | Type | Default | Required | Hidden | | ------------------------ | ----------------------------------------------------------------- | --------- | ------- | -------- | ------ | | `version` | Display version and exit. | `boolean` | | | True | -| `publish_dir_mode` | Method used to save pipeline results to output directory. | `string` | copy | | True | -| `email_on_fail` | Email address for completion summary, only when pipeline fails. | `string` | | | True | +| `publish_dir_mode` | Method used to save pipeline results to output directory. | `string` | +| copy | | True | +| `email_on_fail` | Email address for completion summary, only when pipeline fails. | `string` | +| | True | | `plaintext_email` | Send plain-text email instead of HTML. | `boolean` | | | True | -| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB | | True | +| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | +| `string` | 25.MB | | True | | `monochrome_logs` | Do not use coloured log outputs. | `boolean` | | | True | | `hook_url` | Incoming hook URL for messaging service | `string` | | | True | - -## Other parameters - -| Parameter | Description | Type | Default | Required | Hidden | -| ----------------------------- | ----------- | --------- | ------- | -------- | ------ | -| `add_attrs_to_gffread_fastas` | | `boolean` | | | | diff --git a/nextflow_schema.json b/nextflow_schema.json index 2cc3f8d..2092f00 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -286,6 +286,11 @@ "type": "boolean", "description": "Save BRAKER files", "fa_icon": "fas fa-question-circle" + }, + "add_attrs_to_proteins_cds_fastas": { + "type": "boolean", + "description": "Add gff attributes to proteins/cDNA/cds fasta", + "fa_icon": "fas fa-question-circle" } } }, @@ -433,10 +438,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "add_attrs_to_proteins_cds_fastas": { - "type": "boolean" - } - } + ] }