From a7164bd4207e2a4fa4739a2e15e9f523a481684b Mon Sep 17 00:00:00 2001 From: Regan Date: Thu, 24 Jun 2021 14:24:00 +1200 Subject: [PATCH 1/2] Updated schema --- nextflow_schema.json | 70 +++++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 40 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 843191e4..0793b4a7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -287,12 +287,14 @@ "libtype": { "type": "string", "description": "Options for setting the library type. A = automatic detection", - "fa_icon": "fas fa-sliders-h" + "fa_icon": "fas fa-sliders-h", + "default": "A" }, "incompatPrior": { - "type": "integer", + "type": "string", "description": "By default, this is set to 0.0, to ensure that only mappings or alignments that are compatible with the specified library type are considered by Salmon", - "fa_icon": "fas fa-sliders-h" + "fa_icon": "fas fa-sliders-h", + "default": "0.0" }, "generate_salmon_uniq_ambig": { "type": "boolean", @@ -309,7 +311,7 @@ "gene_feature_gff_to_create_transcriptome_pathogen": { "type": "string", "default": "gene,sRNA,tRNA,rRNA", - "description": "The pipeline uses gene features from the 3rd column of the pathogen annotative fikle (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as `gene`, `sRNA`, `tRNA` and `rRNA` from the `--gff_pathogen` file. Should be a comma-separated string.", + "description": "The pipeline uses gene features from the 3rd column of the pathogen annotative file (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as `gene`, `sRNA`, `tRNA` and `rRNA` from the `--gff_pathogen` file. Should be a comma-separated string.", "fa_icon": "fas fa-sliders-h" }, "gene_attribute_gff_to_create_transcriptome_host": { @@ -485,7 +487,7 @@ "limitBAMsortRAM": { "type": "integer", "description": "Option to limit RAM when sorting BAM file. If 0, will be set to the genome index size, which can be quite large when running on a desktop or laptop", - "default": "0", + "default": 0, "fa_icon": "fas fa-sliders-h" }, "winAnchorMultimapNmax": { @@ -499,6 +501,28 @@ "default": 100, "description": "Option to specify the length of the donor/acceptor sequence on each side of the junctions used in constructing the splice junctions database. By default the option is set to 100. However, we recommend setting a value depending on the read length: read/mate length - 1.", "fa_icon": "fas fa-sliders-h" + }, + "outWigType": { + "type": "string", + "default": "None", + "description": "Used to generate signal outputs, such as \"wiggle\" and \"bedGraph\".", + "fa_icon": "fas fa-sliders-h" + }, + "outWigStrand": { + "type": "string", + "default": "Stranded", + "description": "Options are Stranded or Unstranded when defining the strandedness of wiggle/bedGraph output", + "fa_icon": "fas fa-sliders-h" + }, + "star_index_params": { + "type": "string", + "description": "Set of additional parameters for creating an index with STAR", + "fa_icon": "fas fa-ellipsis-h" + }, + "star_alignment_params": { + "type": "string", + "description": "Set of additional parameters for alignment with STAR", + "fa_icon": "fas fa-ellipsis-h" } }, "fa_icon": "fas fa-star" @@ -528,37 +552,6 @@ }, "fa_icon": "fas fa-star" }, - "star_htseq": { - "title": "STAR - HTseq", - "type": "object", - "description": "Parameters available for STAR - HTSeq", - "default": "", - "properties": { - "outWigType": { - "type": "string", - "default": "None", - "description": "Used to generate signal outputs, such as \"wiggle\" and \"bedGraph\".", - "fa_icon": "fas fa-sliders-h" - }, - "outWigStrand": { - "type": "string", - "default": "Stranded", - "description": "Options are Stranded or Unstranded when defining the strandedness of wiggle/bedGraph output", - "fa_icon": "fas fa-sliders-h" - }, - "star_index_params": { - "type": "string", - "description": "Set of additional parameters for creating an index with STAR", - "fa_icon": "fas fa-ellipsis-h" - }, - "star_alignment_params": { - "type": "string", - "description": "Set of additional parameters for alignment with STAR", - "fa_icon": "fas fa-ellipsis-h" - } - }, - "fa_icon": "fas fa-star" - }, "htseq_general": { "title": "HTSeq - general", "type": "object", @@ -838,9 +831,6 @@ { "$ref": "#/definitions/star_salmon_alignment_based_mode" }, - { - "$ref": "#/definitions/star_htseq" - }, { "$ref": "#/definitions/htseq_general" }, @@ -857,4 +847,4 @@ "$ref": "#/definitions/institutional_config_options" } ] -} +} \ No newline at end of file From ad445ca1ec5a57b6cb927f145120877091c51b58 Mon Sep 17 00:00:00 2001 From: Regan Date: Thu, 24 Jun 2021 14:31:04 +1200 Subject: [PATCH 2/2] Removed params from readme --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 477098b2..ef31a8a0 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,6 @@ The nf-core/dualrnaseq pipeline comes with documentation about the pipeline, fou 2. Pipeline configuration * [Local installation](https://nf-co.re/usage/local_installation) * [Adding your own system config](https://nf-co.re/usage/adding_own_config) - * [Parameters](docs/parameters.md) 3. [Running the pipeline](docs/usage.md) 4. [Output and how to interpret the results](docs/output.md) 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)