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feat: add new measles workflow
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‎catalog/output/workflows.json‎

Lines changed: 50 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,28 @@
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"name": "Variant calling",
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"showComingSoon": true,
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"workflows": [
8+
{
9+
"iwcId": "generic-non-segmented-viral-variant-calling-main",
10+
"parameters": [
11+
{
12+
"key": "Paired collection of sequencing data",
13+
"variable": "SANGER_READ_RUN_PAIRED"
14+
},
15+
{
16+
"key": "Reference annotation",
17+
"variable": "GENE_MODEL_URL"
18+
},
19+
{
20+
"key": "Fasta reference genome",
21+
"variable": "ASSEMBLY_FASTA_URL"
22+
}
23+
],
24+
"ploidy": "ANY",
25+
"taxonomyId": "11158",
26+
"trsId": "#workflow/github.com/iwc-workflows/generic-non-segmented-viral-variant-calling/main/versions/v0.1",
27+
"workflowDescription": "Variant calling and consensus sequence generation for batches of Illumina PE sequenced viruses with uncomplicated and stable genome structure (like e.g. Morbilliviruses). It can handle both ampliconic and non-ampliconic data.",
28+
"workflowName": "Variant calling and consensus construction from paired end short read data of non-segmented viral genomes"
29+
},
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{
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"iwcId": "haploid-variant-calling-wgs-pe-main",
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"parameters": [
@@ -115,7 +137,7 @@
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],
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"ploidy": "ANY",
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"taxonomyId": null,
118-
"trsId": "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex/versions/v0.6.2",
140+
"trsId": "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex/versions/v0.6.3",
119141
"workflowDescription": "Comprehensive preprocessing for 10X Genomics CellPlex multiplexed single-cell RNA-seq data. Processes Cell Multiplexing Oligo (CMO) FASTQ files with CITE-seq-Count including required CellPlex-specific translation steps. Simultaneously processes gene expression FASTQ files with STARsolo and DropletUtils for alignment and cell filtering, and formats outputs for seamless import into Seurat/Scanpy (Read10X function).",
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"workflowName": "Single-Cell RNA-seq Preprocessing: 10X Genomics CellPlex Multiplexed Samples"
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},
@@ -137,7 +159,7 @@
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],
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"ploidy": "ANY",
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"taxonomyId": null,
140-
"trsId": "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3/versions/v0.6.2",
162+
"trsId": "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3/versions/v0.6.3",
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"workflowDescription": "Complete preprocessing pipeline for 10X Genomics v3 single-cell RNA-seq data. Aligns raw FASTQ files using STARsolo, performs cell calling and quality filtering with DropletUtils, and formats outputs for seamless import into Seurat/Scanpy (Read10X function).",
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"workflowName": "Single-Cell RNA-seq Preprocessing: 10X Genomics v3 to Seurat and Scanpy Compatible Format"
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},
@@ -225,8 +247,8 @@
225247
],
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"ploidy": "ANY",
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"taxonomyId": null,
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"trsId": "#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.14",
229-
"workflowDescription": "Complete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.",
250+
"trsId": "#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.15",
251+
"workflowDescription": "Complete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.",
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"workflowName": "ChIP-seq Analysis: Paired-End Read Processing"
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},
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{
@@ -243,8 +265,8 @@
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],
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"ploidy": "ANY",
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"taxonomyId": null,
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"trsId": "#workflow/github.com/iwc-workflows/chipseq-sr/main/versions/v0.14",
247-
"workflowDescription": "Complete ChIP-seq analysis for single-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2 uses either a fixed extension parameter or built-in model to identify protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.",
268+
"trsId": "#workflow/github.com/iwc-workflows/chipseq-sr/main/versions/v0.15",
269+
"workflowDescription": "Complete ChIP-seq analysis for single-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2 uses either a fixed extension parameter or built-in model to identify protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.",
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"workflowName": "ChIP-seq Analysis: Single-End Read Processing"
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},
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{
@@ -282,6 +304,28 @@
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"name": "Consensus sequences",
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"showComingSoon": false,
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"workflows": [
307+
{
308+
"iwcId": "generic-non-segmented-viral-variant-calling-main",
309+
"parameters": [
310+
{
311+
"key": "Paired collection of sequencing data",
312+
"variable": "SANGER_READ_RUN_PAIRED"
313+
},
314+
{
315+
"key": "Reference annotation",
316+
"variable": "GENE_MODEL_URL"
317+
},
318+
{
319+
"key": "Fasta reference genome",
320+
"variable": "ASSEMBLY_FASTA_URL"
321+
}
322+
],
323+
"ploidy": "ANY",
324+
"taxonomyId": "11158",
325+
"trsId": "#workflow/github.com/iwc-workflows/generic-non-segmented-viral-variant-calling/main/versions/v0.1",
326+
"workflowDescription": "Variant calling and consensus sequence generation for batches of Illumina PE sequenced viruses with uncomplicated and stable genome structure (like e.g. Morbilliviruses). It can handle both ampliconic and non-ampliconic data.",
327+
"workflowName": "Variant calling and consensus construction from paired end short read data of non-segmented viral genomes"
328+
},
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{
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"iwcId": "pox-virus-amplicon-main",
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"parameters": [

‎catalog/source/workflows.yml‎

Lines changed: 58 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
# yaml-language-server: $schema=../schema/generated/workflows.json
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workflows:
32
- trs_id: "#workflow/github.com/iwc-workflows/annotation-maker/main/versions/v0.1"
43
categories: []
@@ -30,7 +29,7 @@ workflows:
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class: File
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active: false
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iwc_id: annotation-maker-main
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- trs_id: "#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.2"
32+
- trs_id: "#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.3"
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categories:
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- ASSEMBLY
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workflow_name: Genome assembly with Flye
@@ -61,10 +60,10 @@ workflows:
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- key: reference_genome
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variable: ASSEMBLY_ID
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- key: PE fastq input
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variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
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collection_type: list:paired
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variable: SANGER_READ_RUN_PAIRED
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- key: effective_genome_size
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type_guide:
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class: integer
@@ -94,13 +93,11 @@ workflows:
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class: integer
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active: false
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iwc_id: average-bigwig-between-replicates-main
97-
- trs_id: "#workflow/github.com/iwc-workflows/bacterial-genome-assembly/main/versions/v1.1.7"
96+
- trs_id: "#workflow/github.com/iwc-workflows/bacterial-genome-assembly/main/versions/v2.0"
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categories:
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- ASSEMBLY
10099
workflow_name: Bacterial Genome Assembly using Shovill
101-
workflow_description:
102-
Assembly of bacterial paired-end short read data with generation
103-
of quality metrics and reports
100+
workflow_description: Assembly of bacterial paired-end short read data
104101
ploidy: ANY
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parameters:
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- key: Input adapter trimmed sequence reads (forward)
@@ -216,14 +213,14 @@ workflows:
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class: float
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active: false
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iwc_id: brew3r-main
219-
- trs_id: "#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.14"
216+
- trs_id: "#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.15"
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categories:
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- REGULATION
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workflow_name: "ChIP-seq Analysis: Paired-End Read Processing"
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workflow_description:
224221
Complete ChIP-seq analysis for paired-end sequencing data.
225222
Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference
226-
genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs
223+
genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs
227224
only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA
228225
binding sites. Generates alignment files, peak calls, and quality metrics for
229226
downstream analysis.
@@ -232,10 +229,10 @@ workflows:
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- key: reference_genome
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variable: ASSEMBLY_ID
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- key: PE fastq input
232+
variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
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collection_type: list:paired
238-
variable: SANGER_READ_RUN_PAIRED
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- key: adapter_forward
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type_guide:
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class: text
@@ -250,14 +247,14 @@ workflows:
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class: boolean
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active: true
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iwc_id: chipseq-pe-main
253-
- trs_id: "#workflow/github.com/iwc-workflows/chipseq-sr/main/versions/v0.14"
250+
- trs_id: "#workflow/github.com/iwc-workflows/chipseq-sr/main/versions/v0.15"
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categories:
255252
- REGULATION
256253
workflow_name: "ChIP-seq Analysis: Single-End Read Processing"
257254
workflow_description:
258255
Complete ChIP-seq analysis for single-end sequencing data.
259256
Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference
260-
genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2
257+
genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2
261258
uses either a fixed extension parameter or built-in model to identify protein-DNA
262259
binding sites. Generates alignment files, peak calls, and quality metrics for
263260
downstream analysis.
@@ -266,10 +263,10 @@ workflows:
266263
- key: reference_genome
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variable: ASSEMBLY_ID
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- key: SR fastq input
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variable: SANGER_READ_RUN_SINGLE
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type_guide:
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class: Collection
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collection_type: list
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variable: SANGER_READ_RUN_SINGLE
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- key: adapter_forward
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type_guide:
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class: text
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- key: reference_genome
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variable: ASSEMBLY_ID
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- key: PE fastq input
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variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
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collection_type: list:paired
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variable: SANGER_READ_RUN_PAIRED
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- key: adapter_forward
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type_guide:
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class: text
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class: boolean
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active: true
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iwc_id: cutandrun-main
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- trs_id: "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex/versions/v0.6.2"
402+
- trs_id: "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex/versions/v0.6.3"
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categories:
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- TRANSCRIPTOMICS
408405
workflow_name:
@@ -445,7 +442,7 @@ workflows:
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class: integer
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active: true
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iwc_id: fastq-to-matrix-10x-scrna-seq-fastq-to-matrix-10x-cellplex
448-
- trs_id: "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3/versions/v0.6.2"
445+
- trs_id: "#workflow/github.com/iwc-workflows/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3/versions/v0.6.3"
449446
categories:
450447
- TRANSCRIPTOMICS
451448
workflow_name:
@@ -463,10 +460,10 @@ workflows:
463460
- key: gtf
464461
variable: GENE_MODEL_URL
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- key: fastq PE collection
463+
variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
468466
collection_type: list:paired
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variable: SANGER_READ_RUN_PAIRED
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- key: cellranger_barcodes_3M-february-2018.txt
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type_guide:
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class: File
@@ -475,6 +472,44 @@ workflows:
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class: boolean
476473
active: true
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iwc_id: fastq-to-matrix-10x-scrna-seq-fastq-to-matrix-10x-v3
475+
- trs_id: "#workflow/github.com/iwc-workflows/generic-non-segmented-viral-variant-calling/main/versions/v0.1"
476+
categories:
477+
- CONSENSUS_SEQUENCES
478+
- VARIANT_CALLING
479+
workflow_name:
480+
Variant calling and consensus construction from paired end short
481+
read data of non-segmented viral genomes
482+
workflow_description:
483+
Variant calling and consensus sequence generation for batches
484+
of Illumina PE sequenced viruses with uncomplicated and stable genome structure
485+
(like e.g. Morbilliviruses). It can handle both ampliconic and non-ampliconic data.
486+
ploidy: ANY
487+
taxonomy_id: 11158
488+
parameters:
489+
- key: Paired collection of sequencing data
490+
type_guide:
491+
class: Collection
492+
collection_type: list:paired
493+
variable: SANGER_READ_RUN_PAIRED
494+
- key: Reference annotation
495+
type_guide:
496+
class: File
497+
variable: GENE_MODEL_URL
498+
- key: Fasta reference genome
499+
type_guide:
500+
class: File
501+
variable: ASSEMBLY_FASTA_URL
502+
- key: Primer scheme (optional)
503+
type_guide:
504+
class: File
505+
- key: Supporting read fraction to call variant
506+
type_guide:
507+
class: float
508+
- key: Minimum quality score to consider base for variant calling
509+
type_guide:
510+
class: integer
511+
active: true
512+
iwc_id: generic-non-segmented-viral-variant-calling-main
478513
- trs_id: "#workflow/github.com/iwc-workflows/generic-variant-calling-wgs-pe/main/versions/v0.1.1"
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categories:
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- VARIANT_CALLING
@@ -485,12 +520,12 @@ workflows:
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ploidy: ANY
486521
parameters:
487522
- key: Paired Collection
523+
variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
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ext:
491527
- fastqsanger
492528
- fastqsanger.gz
493-
variable: SANGER_READ_RUN_PAIRED
494529
- key: GenBank genome
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type_guide:
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class: File
@@ -909,10 +944,10 @@ workflows:
909944
- key: GTF file of annotation
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variable: GENE_MODEL_URL
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- key: Collection paired FASTQ files
947+
variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
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collection_type: list:paired
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variable: SANGER_READ_RUN_PAIRED
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- key: Forward adapter
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type_guide:
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class: text
@@ -958,10 +993,10 @@ workflows:
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- key: GTF file of annotation
959994
variable: GENE_MODEL_URL
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- key: Collection of FASTQ files
996+
variable: SANGER_READ_RUN_SINGLE
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type_guide:
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class: Collection
963999
collection_type: list
964-
variable: SANGER_READ_RUN_SINGLE
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- key: Forward adapter
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type_guide:
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class: text
@@ -1024,7 +1059,7 @@ workflows:
10241059
ext: bed
10251060
active: false
10261061
iwc_id: sars-cov-2-ont-artic-variant-calling-covid-19-artic-ont
1027-
- trs_id: "#workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/versions/v0.2.3"
1062+
- trs_id: "#workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE/versions/v0.3.1"
10281063
categories:
10291064
- VARIANT_CALLING
10301065
workflow_name: SARS-CoV-2 Illumina Amplicon pipeline - iVar based
@@ -1065,12 +1100,12 @@ workflows:
10651100
taxonomy_id: 694009
10661101
parameters:
10671102
- key: Paired Collection
1103+
variable: SANGER_READ_RUN_PAIRED
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type_guide:
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class: Collection
10701106
ext:
10711107
- fastqsanger
10721108
- fastqsanger.gz
1073-
variable: SANGER_READ_RUN_PAIRED
10741109
- key: NC_045512.2 FASTA sequence of SARS-CoV-2
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variable: ASSEMBLY_FASTA_URL
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- key: ARTIC primer BED
@@ -1108,12 +1143,12 @@ workflows:
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taxonomy_id: 694009
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parameters:
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- key: Paired Collection
1146+
variable: SANGER_READ_RUN_PAIRED
11111147
type_guide:
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class: Collection
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ext:
11141150
- fastqsanger
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- fastqsanger.gz
1116-
variable: SANGER_READ_RUN_PAIRED
11171152
- key: NC_045512.2 FASTA sequence of SARS-CoV-2
11181153
variable: ASSEMBLY_FASTA_URL
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active: true

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