Commit 03ccd447 authored by jlopez's avatar jlopez
Browse files

Clean tools

parent 09e0def9
......@@ -16,9 +16,9 @@
command: vcftoolz compare,
category: "vcf_postprocess",
output_dir: compare_vcfs,
inputs: [{ name: vcfs }],
inputs: [{ name: vcfs, type: "vcf" }],
outputs: [
{ name: "stats", file: "stats.txt", description: "Results of vcftoolz compare" }
{ name: "stats", type: "txt", file: "stats.txt", description: "Results of vcftoolz compare" }
],
options:
[
......
......@@ -13,15 +13,16 @@
[
{
name: compare_vcfs_isec,
cname: "Compare VCFs (bcftools)",
command: bcftools isec,
category: "vcf_postprocess",
output_dir: compare_vcfs_isec,
inputs: [{ name: vcfs }],
inputs: [{ name: vcfs, type: "vcf" }],
outputs: [
{ name: sites , file: "sites.txt", description: "Results of bcftools isec" },
{ name: snps , file: "snps.txt", description: "Matrix of intersections" },
{ name: common , file: "common.txt", description: "Common positions in all VCFs" },
{ name: common_vcf , file: "output_common_only.vcf.gz", description: "VCF of common positions in all VCFs" }
{ name: sites, type: "txt" , file: "sites.txt", description: "Results of bcftools isec" },
{ name: snps, type: "txt" , file: "snps.txt", description: "Matrix of intersections" },
{ name: common, type: "txt" , file: "common.txt", description: "Common positions in all VCFs" },
{ name: common_vcf, type: "vcf.gz" , file: "output_common_only.vcf.gz", description: "VCF of common positions in all VCFs" }
],
options:
[
......
......@@ -16,32 +16,32 @@
command: ~,
category: "metabarcoding",
output_dir: dada2,
inputs: [{ name: read }, { name: read2 }],
inputs: [{ name: read, type: "reads" }, { name: read2, type: "reads" }],
outputs: [
{ name: qualityForward, file: "Quality_forward_mqc.png", description: "Quality graph of the forward reads of the first two samples" },
{ name: qualityReverse, file: "Quality_reverse_mqc.png", description: "Quality graph of the reverse reads of the first two samples" },
{ name: filter_and_trim_out, file: "filter_and_trim_out.rds", description: "Post-filter and trimming report" },
{ name: filtFs, file: "filtered/{sample}_F_filt.fastq.gz", description: "List of filtered forward reads" },
{ name: filtRs, file: "filtered/{sample}_R_filt.fastq.gz", description: "List of filtered reverse reads" },
{ name: errorsForward, file: "Errors_forward_mqc.png", description: "Error rate graph on forward reads" },
{ name: errorsReverse, file: "Errors_reverse_mqc.png", description: "Error rate graph on reverse reads" },
{ name: errF_rds, file: "errF.rds", description: "Error prediction for forward reads" },
{ name: errR_rds, file: "errR.rds", description: "Error prediction for reverse reads" },
{ name: track, file: "Track_reads_mqc.tsv", description: "Read count in the different steps" },
{ name: seqtab, file: "seqtab.rds", description: "Sequence table" },
{ name: seqtab_nochim_csv, file: "seqtab_nochim.csv", description: "Sequence table after removal of chimeras" },
{ name: seqtab_nochim_rds, file: "seqtab_nochim.rds", description: "Sequence table after removal of chimeras" },
{ name: uniques_nochim, file: "uniques_nochim.fasta", description: "Unique sequences after removal of chimeras" },
{ name: taxa_bootstrap, file: "Taxa_bootstrap_mqc.tsv", description: "Bootstrap of taxa" },
{ name: taxa_rds, file: "taxa.rds", description: "Taxa" },
{ name: otu_table, file: "otu_table.csv", description: "OTU table" },
{ name: tax_table_csv, file: "tax_table.csv", description: "Taxa table" },
{ name: richness, file: "Richness_mqc.png", description: "Richness plot" },
{ name: top20, file: "Top_20_mqc.png", description: "Top 20 OTU" },
{ name: ps_out, file: "ps_out.rds", description: "Phyloseq object" },
{ name: ordination, file: "Ordination_mqc.png", description: "Ordination plot" },
{ name: tax_table_biom, file: "tax_table.qiime.txt", description: "Taxa table for qiime" },
{ name: out_table_biom, file: "otu_table.qiime.biom", description: "OTU table for qiime" },
{ name: qualityForward, type: "png", file: "Quality_forward_mqc.png", description: "Quality graph of the forward reads of the first two samples" },
{ name: qualityReverse, type: "png", file: "Quality_reverse_mqc.png", description: "Quality graph of the reverse reads of the first two samples" },
{ name: filter_and_trim_out, type: "rds", file: "filter_and_trim_out.rds", description: "Post-filter and trimming report" },
{ name: filtFs, type: "fastq.gz", file: "filtered/{sample}_F_filt.fastq.gz", description: "List of filtered forward reads" },
{ name: filtRs, type: "fastq.gz", file: "filtered/{sample}_R_filt.fastq.gz", description: "List of filtered reverse reads" },
{ name: errorsForward, type: "png", file: "Errors_forward_mqc.png", description: "Error rate graph on forward reads" },
{ name: errorsReverse, type: "png", file: "Errors_reverse_mqc.png", description: "Error rate graph on reverse reads" },
{ name: errF_rds, type: "rds", file: "errF.rds", description: "Error prediction for forward reads" },
{ name: errR_rds, type: "rds", file: "errR.rds", description: "Error prediction for reverse reads" },
{ name: track, type: "tsv", file: "Track_reads_mqc.tsv", description: "Read count in the different steps" },
{ name: seqtab, type: "rds", file: "seqtab.rds", description: "Sequence table" },
{ name: seqtab_nochim_csv, type: "csv", file: "seqtab_nochim.csv", description: "Sequence table after removal of chimeras" },
{ name: seqtab_nochim_rds, type: "rds", file: "seqtab_nochim.rds", description: "Sequence table after removal of chimeras" },
{ name: uniques_nochim, type: "fasta", file: "uniques_nochim.fasta", description: "Unique sequences after removal of chimeras" },
{ name: taxa_bootstrap, type: "tsv", file: "Taxa_bootstrap_mqc.tsv", description: "Bootstrap of taxa" },
{ name: taxa_rds, type: "rds", file: "taxa.rds", description: "Taxa" },
{ name: otu_table, type: "csv", file: "otu_table.csv", description: "OTU table" },
{ name: tax_table_csv, type: "csv", file: "tax_table.csv", description: "Taxa table" },
{ name: richness, type: "png", file: "Richness_mqc.png", description: "Richness plot" },
{ name: top20, type: "png", file: "Top_20_mqc.png", description: "Top 20 OTU" },
{ name: ps_out, type: "rds", file: "ps_out.rds", description: "Phyloseq object" },
{ name: ordination, type: "png", file: "Ordination_mqc.png", description: "Ordination plot" },
{ name: tax_table_biom, type: "txt", file: "tax_table.qiime.txt", description: "Taxa table for qiime" },
{ name: out_table_biom, type: "biom", file: "otu_table.qiime.biom", description: "OTU table for qiime" },
],
options:
[
......
......@@ -13,18 +13,19 @@
[
{
name: deseq2,
cname: "Deseq2",
command: ~,
category: "differential_expression",
output_dir: deseq2,
inputs: [{ name: counts }],
inputs: [{ name: counts, type: "tsv" }],
outputs:
[
{ name: de_table, file: de_table.csv, description: "Tableau d'expression différentielle" },
{ name: RData, file: data.RData, description: "Sauvegarde de la session R" },
{ name: PCA, file: PCA_mqc.png, description: "PCA plot" },
{ name: DE_Table, file: DE_Table_mqc.tsv, description: "Tableau d'expression différentielle avec p-value ajustée < 0.1" },
{ name: MA_plot, file: MA_plot_mqc.png, description: "MA-plot log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis)" },
{ name: Heatmap, file: Heatmap_mqc.png, description: "Heatmap" },
{ name: de_table, type: "tsv", file: de_table.csv, description: "Tableau d'expression différentielle" },
{ name: RData, type: "RData", file: data.RData, description: "Sauvegarde de la session R" },
{ name: PCA, type: "png", file: PCA_mqc.png, description: "PCA plot" },
{ name: DE_Table, type: "tsv", file: DE_Table_mqc.tsv, description: "Tableau d'expression différentielle avec p-value ajustée < 0.1" },
{ name: MA_plot, type: "png", file: MA_plot_mqc.png, description: "MA-plot log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis)" },
{ name: Heatmap, type: "png", file: Heatmap_mqc.png, description: "Heatmap" },
],
options:
[
......
......@@ -16,14 +16,14 @@
command: ~,
category: "differential_expression",
output_dir: edger,
inputs: [{ name: counts }],
inputs: [{ name: counts, type: "tsv" }],
outputs:
[
{ name: de_table, file: de_table.csv, description: "Tableau d'expression différentielle" },
{ name: RData, file: data.RData, description: "Sauvegarde de la session R" },
{ name: PCA, file: PCA_mqc.png, description: "PCA plot" },
{ name: Top_genes, file: Top_genes_mqc.tsv, description: "Tableau des top gènes" },
{ name: Heatmap, file: Heatmap_mqc.png, description: "Heatmap" },
{ name: de_table, type: "csv", file: de_table.csv, description: "Tableau d'expression différentielle" },
{ name: RData, type: "RData", file: data.RData, description: "Sauvegarde de la session R" },
{ name: PCA, type: "png", file: PCA_mqc.png, description: "PCA plot" },
{ name: Top_genes, type: "tsv", file: Top_genes_mqc.tsv, description: "Tableau des top gènes" },
{ name: Heatmap, type: "png", file: Heatmap_mqc.png, description: "Heatmap" },
],
options:
[
......
......@@ -12,6 +12,7 @@
[
{
name: interproscan,
cname: "InterProScan",
command: interproscan,
category: "annotation",
output_dir: interproscan,
......
......@@ -13,11 +13,12 @@
[
{
name: kallisto_index,
cname: "Kallisto index",
command: kallisto index,
category: "indexing",
output_dir: kallisto/index,
inputs: [{ name: transcriptome_fasta }],
outputs: [{ name: index, file: index.kidx, description: "Index kallisto" }],
inputs: [{ name: transcriptome_fasta, type: "fasta" }],
outputs: [{ name: index, type: "kidx", file: index.kidx, description: "Index kallisto" }],
options:
[
{
......@@ -30,15 +31,16 @@
},
{
name: kallisto_quant_SE,
cname: "Kallisto quand SE",
command: kallisto quant,
category: "quantification",
output_dir: kallisto/quant,
inputs: [{ name: kallisto_quant_index, file: kallisto/index/index.kidx }, { name: read }],
inputs: [{ name: kallisto_quant_index, type: "kidx", file: kallisto/index/index.kidx }, { name: read, type: "reads" }],
outputs:
[
{ name: h5, file: "{sample}/abundance.h5", description: "Abondances au format h5" },
{ name: counts, file: "{sample}/abundance.tsv", description: "Table d'abondance" },
{ name: run_info, file: "{sample}/run_info.json", description: "Informations sur l'exécution" },
{ name: h5, type: "h5", file: "{sample}/abundance.h5", description: "Abondances au format h5" },
{ name: counts, type: "tsv", file: "{sample}/abundance.tsv", description: "Table d'abondance" },
{ name: run_info, type: "json", file: "{sample}/run_info.json", description: "Informations sur l'exécution" },
],
options:
[
......@@ -76,15 +78,16 @@
},
{
name: kallisto_quant_PE,
cname: "Kallisto quand PE",
command: kallisto quant,
category: "quantification",
output_dir: kallisto/quant,
inputs: [{ name: kallisto_quant_index, file: kallisto/index/index.kidx }, { name: read }, { name: read2 }],
inputs: [{ name: kallisto_quant_index, type: "kidx", file: kallisto/index/index.kidx }, { name: read, type: "reads" }, { name: read2, type: "reads" }],
outputs:
[
{ name: h5, file: "{sample}/abundance.h5", description: "Abondances au format h5" },
{ name: counts, file: "{sample}/abundance.tsv", description: "Table d'abondance" },
{ name: run_info, file: "{sample}/run_info.json", description: "Informations sur l'exécution" },
{ name: h5, type: "h5", file: "{sample}/abundance.h5", description: "Abondances au format h5" },
{ name: counts, type: "tsv", file: "{sample}/abundance.tsv", description: "Table d'abondance" },
{ name: run_info, type: "json", file: "{sample}/run_info.json", description: "Informations sur l'exécution" },
],
options:
[
......
......@@ -13,15 +13,16 @@
[
{
name: mitoz_annotate_SE,
cname: "Mitoz annotate SE",
command: /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate,
category: "annotation",
output_dir: mitoz_annotate_SE,
inputs: [{ name: read }, { name: fasta }],
inputs: [{ name: read, type: "reads" }, { name: fasta, type: "fasta" }],
outputs:
[
{ name: genbank_annots, file: "mitoz_annotate_SE_mitoscaf.fa.gbf", description: "The mitochondrial genome in GenBank format" },
{ name: readme, file: "README.txt", description: "Readme with all output files explained" },
{ name: circos_bam, file: circos.bam, description: "Mapping to determine depth for Circos plot" }
{ name: genbank_annots, type: "fa.gbf", file: "mitoz_annotate_SE_mitoscaf.fa.gbf", description: "The mitochondrial genome in GenBank format" },
{ name: readme, type: "txt", file: "README.txt", description: "Readme with all output files explained" },
{ name: circos_bam, type: "bam", file: circos.bam, description: "Mapping to determine depth for Circos plot" }
],
options:
[
......@@ -59,12 +60,12 @@
command: /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate,
category: "annotation",
output_dir: mitoz_annotate_PE,
inputs: [{ name: read }, { name: read2 }, { name: fasta }],
inputs: [{ name: read, type: "reads" }, { name: read2, type: "reads" }, { name: fasta, type: "fasta" }],
outputs:
[
{ name: genbank_annots, file: "mitoz_annotate_PE_mitoscaf.fa.gbf", description: "The mitochondrial genome in GenBank format" },
{ name: readme, file: "README.txt", description: "Readme with all output files explained" },
{ name: circos_bam, file: circos.bam, description: "Mapping to determine depth for Circos plot" }
{ name: genbank_annots, type: "fa.gbf", file: "mitoz_annotate_SE_mitoscaf.fa.gbf", description: "The mitochondrial genome in GenBank format" },
{ name: readme, type: "txt", file: "README.txt", description: "Readme with all output files explained" },
{ name: circos_bam, type: "bam", file: circos.bam, description: "Mapping to determine depth for Circos plot" }
],
options:
[
......
......@@ -13,19 +13,20 @@
[
{
name: moments,
cname: "Moments",
command: "",
category: "genet_pop",
output_dir: moments,
inputs:
[
{ name: fs_file_name },
{ name: fs_file_name, type: "path" },
#{ pop_file_name: } Path-name to the file describing how individuals map to populations. This file is ignored if datatype is not 'vcf'.
],
outputs: [
{ name: full, file: "moments-full.txt", description: "" },
{ name: easy, file: "moments-easy.txt", description: "" },
{ name: modelsfs, file: "moments-modelsfs.txt", description: "" },
{ name: img, file: "moments_{model}_mqc.png", description: "" }
{ name: full, type: "txt", file: "moments-full.txt", description: "" },
{ name: easy, type: "txt", file: "moments-easy.txt", description: "" },
{ name: modelsfs, type: "txt", file: "moments-modelsfs.txt", description: "" },
{ name: img, type: "png", file: "moments_{model}_mqc.png", description: "" }
],
options:
[
......
......@@ -13,27 +13,28 @@
[
{
name: populations,
cname: "Populations",
command: populations,
category: "population_analysis",
output_dir: populations,
inputs: [{ name: gstacks_dir }],
inputs: [{ name: gstacks_dir, type: "gstacks_dir" }],
outputs: [
{ name: fstats_pop, file: "populations.fst_{popA}-{popB}.tsv", description: "SNP and haplotype-based F statistics between each populations" },
{ name: fstats_summary, file: "populations.fst_summary.tsv", description: "SNP and haplotype-based F statistics summary" },
{ name: haplotypes_tab, file: populations.haplotypes.tsv, description: "Haplotypes for each sample" },
{ name: phistats_pop, file: "populations.phistats_{popA}-{popB}.tsv", description: "Phi statistics between each populations" },
{ name: phistats_summary, file: "populations.phistats_summary.tsv", description: "Phi statistics summary" },
{ name: vcf, file: "populations.snps.vcf", description: "SNP vcf file" },
{ name: structure, file: "populations.structure", description: "Output in Structure format" },
{ name: genepop_haplotypes, file: "populations.haps.genepop", description: "Haplotypes in GenePop format" },
{ name: genepop_snps, file: "populations.snps.genepop", description: "SNP in GenePop format" },
{ name: plink_map, file: "populations.plink.map", description: "Genotypes in PLINK format" },
{ name: plink_ped, file: "populations.plink.ped", description: "Genotypes in PLINK format" },
{ name: radpainter_haplotypes, file: "populations.haps.radpainter", description: "Haplotypes fineRADstructure/RADpainter format" },
{ name: PCA_Eigenvalues_mqc, file: PCA_Eigenvalues_mqc.txt ,description: "PCA eigenvalues" },
{ name: PCA_First2axis_mqc, file: PCA_First2axis_mqc.yaml ,description: "PCA plot on first 2 axis" },
{ name: Mean_Pairwise_Pop_FST_mqc, file: Mean_Pairwise_Pop_FST_mqc.csv ,description: "Mean pairwise population Fstats" },
{ name: IBS_mqc, file: IBS_mqc.png ,description: "IBS heatmap" },
{ name: fstats_pop, type: "tsv", file: "populations.fst_{popA}-{popB}.tsv", description: "SNP and haplotype-based F statistics between each populations" },
{ name: fstats_summary, type: "tsv", file: "populations.fst_summary.tsv", description: "SNP and haplotype-based F statistics summary" },
{ name: haplotypes_tab, type: "tsv", file: populations.haplotypes.tsv, description: "Haplotypes for each sample" },
{ name: phistats_pop, type: "tsv", file: "populations.phistats_{popA}-{popB}.tsv", description: "Phi statistics between each populations" },
{ name: phistats_summary, type: "tsv", file: "populations.phistats_summary.tsv", description: "Phi statistics summary" },
{ name: vcf, type: "vcf", file: "populations.snps.vcf", description: "SNP vcf file" },
{ name: structure, type: "structure", file: "populations.structure", description: "Output in Structure format" },
{ name: genepop_haplotypes, type: "genepop", file: "populations.haps.genepop", description: "Haplotypes in GenePop format" },
{ name: genepop_snps, type: "genepop", file: "populations.snps.genepop", description: "SNP in GenePop format" },
{ name: plink_map, type: "map", file: "populations.plink.map", description: "Genotypes in PLINK format" },
{ name: plink_ped, type: "ped", file: "populations.plink.ped", description: "Genotypes in PLINK format" },
{ name: radpainter_haplotypes, type: "radpainter", file: "populations.haps.radpainter", description: "Haplotypes fineRADstructure/RADpainter format" },
{ name: PCA_Eigenvalues_mqc, type: "txt", file: PCA_Eigenvalues_mqc.txt ,description: "PCA eigenvalues" },
{ name: PCA_First2axis_mqc, type: "yaml", file: PCA_First2axis_mqc.yaml ,description: "PCA plot on first 2 axis" },
{ name: Mean_Pairwise_Pop_FST_mqc, type: "csv", file: Mean_Pairwise_Pop_FST_mqc.csv ,description: "Mean pairwise population Fstats" },
{ name: IBS_mqc, type: "png", file: IBS_mqc.png ,description: "IBS heatmap" },
],
options:
[
......
......@@ -14,11 +14,12 @@
[
{
name: salmon_index,
cname: "Salmon index",
command: salmon index,
category: "indexing",
output_dir: salmon/index,
inputs: [{ name: transcriptome_fasta }],
outputs: [{ name: index, directory: indexDir, description: "Index Salmon" }],
inputs: [{ name: transcriptome_fasta, type: "fasta" }],
outputs: [{ name: index, type: "sidx", directory: indexDir, description: "Index Salmon" }],
options:
[
{
......@@ -42,15 +43,16 @@
},
{
name: salmon_quant_SE,
cname: "Salmon quand SE",
command: salmon quant,
category: "quantification",
output_dir: salmon/quant,
inputs: [{ name: index, directory: salmon/index/indexDir }, { name: read }],
inputs: [{ name: index, type: "sidx", directory: salmon/index/indexDir }, { name: read, type: "reads" }],
outputs:
[
{ name: lib_counts, file: "salmon/quant/{sample}/lib_format_counts.json", description: "Comptages au format JSON" },
{ name: counts, file: "salmon/quant/{sample}/quant.sf", description: "Fichier de compte Salmon" },
{ name: run_info, file: "salmon/quant/{sample}/cmd_info.json", description: "Informations sur l'exécution" },
{ name: lib_counts, type: "json", file: "salmon/quant/{sample}/lib_format_counts.json", description: "Comptages au format JSON" },
{ name: counts, type: "sf", file: "salmon/quant/{sample}/quant.sf", description: "Fichier de compte Salmon" },
{ name: run_info, type: "json", file: "salmon/quant/{sample}/cmd_info.json", description: "Informations sur l'exécution" },
],
options:
[
......@@ -68,15 +70,16 @@
},
{
name: salmon_quant_PE,
cname: "Salmon quand PE",
command: salmon quant,
category: "quantification",
output_dir: salmon/quant,
inputs: [{ name: index, file: salmon/index/indexDir }, { name: read }, { name: read2 }],
inputs: [{ name: index, file: salmon/index/indexDir, type: "sidx" }, { name: read, type: "reads" }, { name: read2, type: "reads" }],
outputs:
[
{ name: lib_counts, file: "salmon/quant/{sample}/lib_format_counts.json", description: "Comptages au format JSON" },
{ name: counts, file: "salmon/quant/{sample}/quant.sf", description: "Fichier de compte Salmon" },
{ name: run_info, file: "salmon/quant/{sample}/cmd_info.json", description: "Informations sur l'exécution" },
{ name: lib_counts, type: "json", file: "salmon/quant/{sample}/lib_format_counts.json", description: "Comptages au format JSON" },
{ name: counts, type: "sf", file: "salmon/quant/{sample}/quant.sf", description: "Fichier de compte Salmon" },
{ name: run_info, type: "json", file: "salmon/quant/{sample}/cmd_info.json", description: "Informations sur l'exécution" },
],
options:
[
......
......@@ -13,6 +13,7 @@
[
{
name: simul_coal,
cname: "Coalescent Simulation",
command: "",
category: "genet_pop",
output_dir: simul_coal,
......@@ -20,7 +21,7 @@
# no input, simulate data from parameters
],
outputs: [
{ name: msout, file: "msout", description: "msout" }
{ name: msout, type: "msout", file: "msout", description: "msout" }
],
options:
[
......
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