Commit 863d2c31 authored by jlopez's avatar jlopez
Browse files

Add caterory to tool & fix warning

parent 8d7d5313
......@@ -14,6 +14,7 @@
{
name: Picard_MarkDuplicates,
command: java -jar /opt/biotools/bin/picard.jar MarkDuplicates,
category: "bam_correction",
output_dir: Picard_MarkDuplicates,
inputs: [],
outputs: [],
......
......@@ -14,6 +14,7 @@
{
name: "bcftools_mpileup_and_call",
command: "bcftools",
category: variant_calling,
output_dir: "bcftools_call",
inputs:
[
......
......@@ -14,6 +14,7 @@
{
name: blast_refseq,
command: blastn,
category: "blast",
output_dir: blast_refseq,
inputs: [
{ name: query }
......
......@@ -14,6 +14,7 @@
{
name: bowtie_index,
command: bowtie-build,
category: "indexing",
output_dir: bowtie/index,
inputs: [{ name: genome_fasta }],
outputs: [{ name: index, file: index, description: "Index files for bowtie alignment" }],
......@@ -46,6 +47,7 @@
{
name: bowtie_PE,
command: bowtie,
category: "mapping",
output_dir: bowtie/PE,
inputs: [{ name: read }, { name: read2 }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......@@ -123,6 +125,7 @@
{
name: bowtie_SE,
command: bowtie,
category: "mapping",
output_dir: bowtie/SE,
inputs: [{ name: read }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......
......@@ -14,6 +14,7 @@
{
name: bowtie2_index,
command: bowtie2-build,
category: "indexing",
output_dir: bowtie2/index,
inputs: [{ name: genome_fasta }],
outputs: [{ name: index, file: index, description: "Index files for bowtie2 alignment" }],
......@@ -46,6 +47,7 @@
{
name: bowtie2_PE,
command: bowtie2,
category: "mapping",
output_dir: bowtie2/PE,
inputs: [{ name: read }, { name: read2 }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......@@ -99,6 +101,7 @@
{
name: bowtie2_SE,
command: bowtie2,
category: "mapping",
output_dir: bowtie2/SE,
inputs: [{ name: read }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......
......@@ -14,6 +14,7 @@
{
name: bwa-mem2_index,
command: bwa-mem2 index,
category: "indexing",
output_dir: bwa-mem2/index,
inputs: [{ name: genome_fasta }],
outputs: [{ name: index, file: index, description: "Index files for bwa-mem2 alignment" }],
......@@ -38,6 +39,7 @@
{
name: bwa-mem2_mem_PE,
command: bwa-mem2 mem,
category: "mapping",
output_dir: bwa-mem2/mem/PE,
inputs: [{ name: read }, { name: read2 }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......@@ -65,6 +67,7 @@
{
name: bwa-mem2_mem_SE,
command: bwa-mem2 mem,
category: "mapping",
output_dir: bwa-mem2/mem/SE,
inputs: [{ name: read }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......
......@@ -15,6 +15,7 @@
{
name: bwa_index,
command: bwa index,
category: "indexing",
output_dir: bwa/index,
inputs: [{ name: genome_fasta }],
outputs: [{ name: index, file: index, description: "Index files for bwa alignment" }],
......@@ -52,6 +53,7 @@
{
name: bwa_mem_PE,
command: bwa mem,
category: "mapping",
output_dir: bwa/mem/PE,
inputs: [{ name: read }, { name: read2 }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......@@ -90,6 +92,7 @@
{
name: bwa_mem_SE,
command: bwa mem,
category: "mapping",
output_dir: bwa/mem/SE,
inputs: [{ name: read }, { name: index }],
outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
......
......@@ -14,6 +14,7 @@
{
name: compare_vcfs,
command: vcftoolz compare,
category: "vcf_postprocess",
output_dir: compare_vcfs,
inputs: [{ name: vcfs }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: compare_vcfs_isec,
command: bcftools isec,
category: "vcf_postprocess",
output_dir: compare_vcfs_isec,
inputs: [{ name: vcfs }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: cstacks,
command: cstacks,
category: "stacks",
output_dir: stacks,
inputs: [{ name: tags },{ name: snps },{ name: alleles }],
outputs:
......
......@@ -14,6 +14,7 @@
{
name: cutadapt_PE,
command: cutadapt,
category: "quality",
output_dir: cutadapt_PE,
inputs: [{ name: read }, { name: read2 }],
outputs:
......@@ -79,6 +80,7 @@
{
name: cutadapt_SE,
command: cutadapt,
category: "quality",
output_dir: cutadapt_SE,
inputs: [{ name: read }],
outputs: [{ name: read, file: "{sample}_trimmed.fq.gz", description: "Reads trimmed"}],
......
......@@ -14,6 +14,7 @@
{
name: dada2,
command: ~,
category: "metabarcoding",
output_dir: dada2,
inputs: [{ name: read }, { name: read2 }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: dadi,
command: "",
category: "genet_pop",
output_dir: dadi,
inputs:
[
......
......@@ -3,17 +3,18 @@
name: DeepVariant,
tool_step: "Variant_calling",
article: 10.1038/nbt.4235,
website: https://github.com/google/deepvariant,
git: https://github.com/google/deepvariant,
website: "https://github.com/google/deepvariant",
git: "https://github.com/google/deepvariant",
description: "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.",
version: "0.9.0",
documentation: https://github.com/google/deepvariant/blob/r0.9/docs/README.md,
documentation: "https://github.com/google/deepvariant/blob/r0.9/docs/README.md",
multiqc: "custom",
commands:
[
{
name: deep_variant,
command: python /opt/deepvariant/bin/run_deepvariant.py,
category: variant_calling,
output_dir: deep_variant,
inputs: [{ name: genome_fasta }, { name: bams }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: demultiplexing_astrid_cruaud,
command: "",
category: "other",
output_dir: demultiplexing_astrid_cruaud,
inputs: [{ name: reads }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: deseq2,
command: ~,
category: "differential_expression",
output_dir: deseq2,
inputs: [{ name: counts }],
outputs:
......
......@@ -14,6 +14,7 @@
{
name: edger,
command: ~,
category: "differential_expression",
output_dir: edger,
inputs: [{ name: counts }],
outputs:
......
......@@ -14,6 +14,7 @@
{
name: fastp_PE,
command: fastp,
category: "quality",
output_dir: fastp_PE,
inputs: [{ name: read }, { name: read2 }],
outputs: [
......@@ -98,6 +99,7 @@
{
name: fastp_SE,
command: fastp,
category: "quality",
output_dir: fastp_SE,
inputs: [{ name: read }],
outputs: [
......
......@@ -14,6 +14,7 @@
{
name: fastqc_SE,
command: fastqc,
category: "quality",
output_dir: fastqc_SE,
inputs: [{ name: read }],
outputs:
......@@ -28,6 +29,7 @@
{
name: fastqc_PE,
command: fastqc,
category: "quality",
output_dir: fastqc_PE,
inputs: [{ name: read },{ name: read2 }],
outputs:
......
......@@ -4,9 +4,9 @@
tool_step: "Quality",
description: "FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments",
version: "1.2.11",
website: https://ccb.jhu.edu/software/FLASH/,
website: "https://ccb.jhu.edu/software/FLASH/",
git: "https://sourceforge.net/projects/flashpage/files/",
documentation: https://ccb.jhu.edu/software/FLASH/,
documentation: "https://ccb.jhu.edu/software/FLASH/",
article: 10.1093/bioinformatics/btr507,
multiqc: "custom",
commands:
......@@ -14,6 +14,7 @@
{
name: flash,
command: flash,
category: "sequence_manipulation",
output_dir: flash,
inputs: [{ name: read },{ name: read2 }],
outputs: [
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment