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Commit 3e1c8bb1 authored by MARTIN Pierre's avatar MARTIN Pierre
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{
"01_clean_qc":
[
{"file":"01_1_cleaned_reads/logs/a.no_filter.flagstat", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/c.no_filter.flagstat", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/a_cutadapt.log", "method":"cut_diff"},
{"file":"01_1_cleaned_reads/logs/c_cutadapt.log", "method":"cut_diff"},
{"file":"01_1_cleaned_reads/logs/a_sickle.log", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/c_sickle.log", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/host_filter_flagstat/a.host_filter.flagstat", "method":"diff"},
{"file":"01_1_cleaned_reads/logs/host_filter_flagstat/c.host_filter.flagstat", "method":"diff"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R2_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R2_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/a/a_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/c/c_R1_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/a/a_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/c/c_R2_fastqc.zip", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/a/a_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/c/c_R1_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/a/a_R2_fastqc.html", "method":"not_empty"},
{"file":"01_2_qc/fastqc_raw/c/c_R2_fastqc.html", "method":"not_empty"},
{"file":"01_3_taxonomic_affiliation_reads/a.krona.html", "method":"not_empty"},
{"file":"01_3_taxonomic_affiliation_reads/c.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/a.count_reads_on_contigs.flagstat", "method":"diff"},
{"file":"logs/c.count_reads_on_contigs.flagstat", "method":"diff"},
{"file":"logs/a.count_reads_on_contigs.idxstats", "method":"diff"},
{"file":"logs/c.count_reads_on_contigs.idxstats", "method":"diff"},
{"file":"a_metaspades/a_scaffolds.fasta", "method":"diff"},
{"file":"c_metaspades/c_scaffolds.fasta", "method":"diff"},
{"file":"a_megahit/a_contigs.fa", "method":"diff"},
{"file":"c_megahit/c_contigs.fa", "method":"diff"},
{"file":"a_all_contigs_QC/report.tsv", "method":"diff"},
{"file":"c_all_contigs_QC/report.tsv", "method":"diff"},
{"file":"a_all_contigs_QC/report.html", "method":"not_empty"},
{"file":"c_all_contigs_QC/report.html", "method":"not_empty"}
],
"03_filtering":
[
{"file":"a_select_contigs_cpm10.fasta", "method":"diff"},
{"file":"c_select_contigs_cpm10.fasta", "method":"diff"},
{"file":"a_discard_contigs_cpm10.fasta", "method":"diff"},
{"file":"c_discard_contigs_cpm10.fasta", "method":"diff"},
{"file":"a_select_contigs_QC/report.tsv", "method":"diff"},
{"file":"c_select_contigs_QC/report.tsv", "method":"diff"},
{"file":"a_select_contigs_QC/report.html", "method":"not_empty"},
{"file":"c_select_contigs_QC/report.html", "method":"not_empty"}
],
"04_structural_annot":
[
{"file":"a.annotated.faa", "method":"diff"},
{"file":"c.annotated.faa", "method":"diff"},
{"file":"a.annotated.ffn", "method":"diff"},
{"file":"c.annotated.ffn", "method":"diff"},
{"file":"a.annotated.fna", "method":"diff"},
{"file":"c.annotated.fna", "method":"diff"},
{"file":"a.annotated.gff", "method":"diff"},
{"file":"c.annotated.gff", "method":"diff"},
{"file":"a_prot.len", "method":"diff"},
{"file":"c_prot.len", "method":"diff"}
],
"05_alignment":
[
{"file":"05_1_reads_alignment_on_contigs/a/a_contig.bed", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/c/c_contig.bed", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/a/a.sort.bam.idxstats", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/c/c.sort.bam.idxstats", "method":"diff"},
{"file":"05_1_reads_alignment_on_contigs/a/a.regions.bed.gz", "method":"zdiff"},
{"file":"05_1_reads_alignment_on_contigs/c/c.regions.bed.gz", "method":"zdiff"},
{"file":"05_2_database_alignment/a/a_aln_diamond.m8", "method":"diff"},
{"file":"05_2_database_alignment/c/c_aln_diamond.m8", "method":"diff"}
],
"06_func_annot":
[
{"file":"06_1_clustering/a.cd-hit-est.0.95.fasta", "method":"diff"},
{"file":"06_1_clustering/c.cd-hit-est.0.95.fasta", "method":"diff"},
{"file":"06_1_clustering/a.cd-hit-est.0.95.fasta.clstr", "method":"diff"},
{"file":"06_1_clustering/c.cd-hit-est.0.95.fasta.clstr", "method":"diff"},
{"file":"06_1_clustering/a.cd-hit-est.0.95.table_cluster_contigs.txt", "method":"diff"},
{"file":"06_1_clustering/c.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/c.featureCounts.tsv", "method":"diff"},
{"file":"06_2_quantification/a.featureCounts.tsv", "method":"diff"},
{"file":"06_2_quantification/c.featureCounts.tsv.summary", "method":"diff"},
{"file":"06_2_quantification/a.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/a.best_hit", "method":"diff"},
{"file":"06_3_functional_annotation/c.best_hit", "method":"diff"},
{"file":"06_3_functional_annotation/a_diamond_one2one.emapper.annotations", "method":"no_header_diff"},
{"file":"06_3_functional_annotation/c_diamond_one2one.emapper.annotations", "method":"no_header_diff"},
{"file":"06_3_functional_annotation/a_diamond_one2one.emapper.seed_orthologs", "method":"no_header_diff"},
{"file":"06_3_functional_annotation/c_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":"a/a.percontig.tsv", "method":"diff"},
{"file":"a/a.pergene.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_class.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_family.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_genus.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_order.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_phylum.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_species.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig_by_superkingdom.tsv", "method":"diff"},
{"file":"a/a_quantif_percontig.tsv", "method":"diff"},
{"file":"a/a.warn.tsv", "method":"diff"},
{"file":"a/graphs/a_aln_diamond.m8_contig_taxonomy_level.pdf", "method":"not_empty"},
{"file":"a/graphs/a_aln_diamond.m8_nb_prot_annotated_and_assigned.pdf", "method":"not_empty"},
{"file":"a/graphs/a_aln_diamond.m8_prot_taxonomy_level.pdf", "method":"not_empty"},
{"file":"c/c.percontig.tsv", "method":"diff"},
{"file":"c/c.pergene.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_class.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_family.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_genus.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_order.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_phylum.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_species.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig_by_superkingdom.tsv", "method":"diff"},
{"file":"c/c_quantif_percontig.tsv", "method":"diff"},
{"file":"c/c.warn.tsv", "method":"diff"},
{"file":"c/graphs/c_aln_diamond.m8_contig_taxonomy_level.pdf", "method":"not_empty"},
{"file":"c/graphs/c_aln_diamond.m8_nb_prot_annotated_and_assigned.pdf", "method":"not_empty"},
{"file":"c/graphs/c_aln_diamond.m8_prot_taxonomy_level.pdf", "method":"not_empty"}
]
}
\ No newline at end of file
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