Folder rearrangement.

For RNA-seq and GRO-seq, log and data directories are now subdirectories
of output directories. local_annot_dir also moves as subdirectory of
GRO-seq output.

PRO-seq/PRO-seq.snakefile

@@ -117,8 +117,6 @@ ANNOT_BIOTYPES = config["annot_biotypes"]
 #METAGENE_BIOTYPES=["protein_coding", "DNA_transposons_rmsk", "RNA_transposons_rmsk"]
 METAGENE_BIOTYPES=["protein_coding"]
 ID_LISTS = ["lfc_statuses", "germline_specific", "histone", "spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014"]
-log_dir = config["log_dir"]
-data_dir = config["data_dir"]
 annot_dir = config["annot_dir"]
 gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
 avail_id_lists = set(glob(OPJ(gene_lists_dir, "*_ids.txt")))
@@ -126,11 +124,14 @@ chrom_sizes = get_chrom_sizes(config["genome_size"])
 genomelen = sum(chrom_sizes.values())
 genome_binned = "/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed"
 #gene_lists_dir = config["gene_lists_dir"]
-local_annot_dir = config["local_annot_dir"]
+#local_annot_dir = config["local_annot_dir"]
 aligner = config["aligner"]
 index = config["index"]
 convert_dir = config["convert_dir"]
 output_dir = config["output_dir"]
+log_dir = OPJ(output_dir, "logs")
+data_dir = OPJ(output_dir, "data")
+local_annot_dir = OPJ(output_dir, "annotations")
 # Used to skip some genotype x treatment x replicate number combinations
 # when some of them were not sequenced
 forbidden = {frozenset(wc_comb.items()) for wc_comb in config["missing"]}

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -106,8 +106,6 @@ COND_COLUMNS = pd.DataFrame(CONDITIONS).assign(
 
 BIOTYPES = config["biotypes"]
 ID_LISTS = ["lfc_statuses", "germline_specific", "histone", "spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014"]
-log_dir = config["log_dir"]
-data_dir = config["data_dir"]
 annot_dir = config["annot_dir"]
 gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
 avail_id_lists = set(glob(OPJ(gene_lists_dir, "*_ids.txt")))
@@ -124,6 +122,8 @@ aligner = config["aligner"]
 COUNTERS = ["feature_count"]
 convert_dir = config["convert_dir"]
 output_dir = config["output_dir"]
+log_dir = OPJ(output_dir, "logs")
+data_dir = OPJ(output_dir, "data")
 
 SIZE_FACTORS = ["protein_coding", "miRNA", "median_ratio_to_pseudo_ref"]
 assert set(SIZE_FACTORS).issubset(set(BIOTYPES) | {"median_ratio_to_pseudo_ref"})