Commit 1dbef6d3 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Delete new_files_to_test.json

parent 3e1c8bb1
{
"01_clean_qc":
[
{"file":"01_1_cleaned_reads/logs/{sampleId}.no_filter.flagstat", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/{sampleId}_cutadapt.log", "method":"cut_diff"},
{"file":"01_1_cleaned_reads/logs/{sampleId}_sickle.log", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/host_filter_flagstat/{sampleId}.host_filter.flagstat", "method":"diff"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_{sampleId}/cleaned_{sampleId}_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_{sampleId}/cleaned_{sampleId}_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_{sampleId}/cleaned_{sampleId}_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_{sampleId}/cleaned_{sampleId}_R2_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/{sampleId}/{sampleId}_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/{sampleId}/{sampleId}_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/{sampleId}/{sampleId}_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/{sampleId}/{sampleId}_R2_fastqc.html", "method":"not_empty"},
{"file":"01_3_taxonomic_affiliation_reads/{sampleId}.krona.html", "method":"not_empty"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_class.tsv", "method":"taxo_diff"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_family.tsv", "method":"taxo_diff"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_genus.tsv", "method":"taxo_diff"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_order.tsv", "method":"taxo_diff"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_phylum.tsv", "method":"taxo_diff"},
{"file":"01_3_taxonomic_affiliation_reads/taxo_affi_reads_species.tsv", "method":"taxo_diff"}
],
"02_assembly":
[
{"file":"logs/{sampleId}.count_reads_on_contigs.flagstat", "method":"diff"},
{"file":"logs/{sampleId}.count_reads_on_contigs.idxstats", "method":"diff"},
{"file":"{sampleId}_metaspades/{sampleId}_scaffolds.fasta", "method":"diff"},
{"file":"{sampleId}_megahit/{sampleId}_contigs.fa", "method":"diff"},
{"file":"{sampleId}_all_contigs_QC/report.tsv", "method":"diff"},
{"file":"{sampleId}_all_contigs_QC/report.html", "method":"not_empty"}
],
"03_filtering":
[
{"file":"{sampleId}_select_contigs_cpm10.fasta", "method":"diff"},
{"file":"{sampleId}_discard_contigs_cpm10.fasta", "method":"diff"},
{"file":"{sampleId}_select_contigs_QC/report.tsv", "method":"diff"},
{"file":"{sampleId}_select_contigs_QC/report.html", "method":"not_empty"}
],
"04_structural_annot":
[
{"file":"{sampleId}.annotated.faa", "method":"diff"},
{"file":"{sampleId}.annotated.ffn", "method":"diff"},
{"file":"{sampleId}.annotated.fna", "method":"diff"},
{"file":"{sampleId}.annotated.gff", "method":"diff"},
{"file":"{sampleId}_prot.len", "method":"diff"}
],
"05_alignment":
[
{"file":"05_1_reads_alignment_on_contigs/{sampleId}/{sampleId}_contig.bed", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/{sampleId}/{sampleId}.sort.bam.idxstats", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/{sampleId}/{sampleId}.regions.bed.gz", "method":"zdiff"},
{"file":"05_2_database_alignment/{sampleId}/{sampleId}_aln_diamond.m8", "method":"diff"}
],
"06_func_annot":
[
{"file":"06_1_clustering/{sampleId}.cd-hit-est.0.95.fasta", "method":"diff"},
{"file":"06_1_clustering/{sampleId}.cd-hit-est.0.95.fasta.clstr", "method":"diff"},
{"file":"06_1_clustering/{sampleId}.cd-hit-est.0.95.table_cluster_contigs.txt", "method":"diff"},
{"file":"06_1_clustering/All-cd-hit-est.0.95.fasta", "method":"diff"},
{"file":"06_1_clustering/All-cd-hit-est.0.95.fasta.clstr", "method":"diff"},
{"file":"06_1_clustering/table_clstr.txt", "method":"diff"},
{"file":"06_2_quantification/{sampleId}.featureCounts.tsv", "method":"diff"},
{"file":"06_2_quantification/{sampleId}.featureCounts.tsv.summary", "method":"diff"},
{"file":"06_2_quantification/Clusters_Count_table_all_samples.txt", "method":"diff"},
{"file":"06_2_quantification/Correspondence_global_clstr_genes.txt", "method":"diff"},
{"file":"06_3_functional_annotation/{sampleId}.best_hit", "method":"diff"},
{"file":"06_3_functional_annotation/{sampleId}_diamond_one2one.emapper.annotations", "method":"no_header_diff"},
{"file":"06_3_functional_annotation/{sampleId}_diamond_one2one.emapper.seed_orthologs", "method":"no_header_diff"},
{"file":"06_3_functional_annotation/GOs_abundance.tsv", "method":"diff"},
{"file":"06_3_functional_annotation/KEGG_ko_abundance.tsv", "method":"diff"},
{"file":"06_3_functional_annotation/KEGG_Module_abundance.tsv", "method":"diff"},
{"file":"06_3_functional_annotation/KEGG_Pathway_abundance.tsv", "method":"diff"},
{"file":"06_3_functional_annotation/PFAM_abundance.tsv", "method":"diff"},
{"file":"06_3_functional_annotation/Quantifications_and_functional_annotations.tsv", "method":"diff"}
],
"07_taxo_affi":
[
{"file":"quantification_by_contig_lineage_all.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_class.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_family.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_genus.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_order.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_phylum.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_species.tsv", "method":"diff"},
{"file":"quantification_by_contig_lineage_superkingdom.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}.percontig.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}.pergene.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_class.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_family.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_genus.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_order.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_phylum.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_species.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig_by_superkingdom.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}_quantif_percontig.tsv", "method":"diff"},
{"file":"{sampleId}/{sampleId}.warn.tsv", "method":"diff"},
{"file":"{sampleId}/graphs/{sampleId}_aln_diamond.m8_contig_taxonomy_level.pdf", "method":"not_empty"},
{"file":"{sampleId}/graphs/{sampleId}_aln_diamond.m8_nb_prot_annotated_and_assigned.pdf", "method":"not_empty"},
{"file":"{sampleId}/graphs/{sampleId}_aln_diamond.m8_prot_taxonomy_level.pdf", "method":"not_empty"}
]
}
\ No newline at end of file
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