diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile index b56f1546587c98699873869210a20cd486f2757a..c63d6773bf93bdf912391ac80882344e39389c6f 100644 --- a/CLIP/iCLIP.snakefile +++ b/CLIP/iCLIP.snakefile @@ -427,7 +427,7 @@ rule map_on_genome: err = OPJ(log_dir, "{trimmer}", aligner, "map_{read_type}_on_genome", "{lib}_{rep}.err"), threads: 12 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule remap_on_genome: @@ -455,7 +455,7 @@ rule remap_on_genome: err = OPJ(log_dir, "{trimmer}", aligner, "remap_{read_type}_unmapped_on_genome", "{lib}_{rep}.err"), threads: 12 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule sam2indexedbam: @@ -474,7 +474,7 @@ rule sam2indexedbam: resources: mem_mb=4100 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" rule compute_mapping_stats: diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile index f91c701b5e8d57102f8f9b83ec3efe9528e9eb7b..bed3a3a61f5c7a69c3fe9790d64337df13cd4743 100644 --- a/Degradome-seq/Degradome-seq.snakefile +++ b/Degradome-seq/Degradome-seq.snakefile @@ -170,7 +170,7 @@ rule map_on_genome: threads: 4 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule sam2indexedbam: @@ -189,7 +189,7 @@ rule sam2indexedbam: resources: mem_mb=4100 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" def biotype2annot(wildcards): @@ -396,7 +396,7 @@ rule compute_RPK: # rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index") # rpk.to_csv(output.rpk_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_RPK" + f"file://{wrappers_dir[0]}/compute_RPK" # Compute TPM using total number of mappers divided by genome length @@ -418,7 +418,7 @@ rule compute_TPM: # tpm = 1000000 * rpk / rpk.sum() # tpm.to_csv(output.tpm_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_TPM" + f"file://{wrappers_dir[0]}/compute_TPM" # TODO: Is it better to compute the mean and then the fold of the means? diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile index b1d73f0428049baa1a4837f56cd33a3fdcd95f2a..1e70b4e6322aa005d5b7b0bc4acece0b47d85ea5 100644 --- a/PRO-seq/PRO-seq.snakefile +++ b/PRO-seq/PRO-seq.snakefile @@ -491,7 +491,7 @@ rule map_on_genome: # eval ${{cmd}} 1>> {log.log} 2>> {log.err} # """ wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule sam2indexedbam: @@ -510,7 +510,7 @@ rule sam2indexedbam: resources: mem_mb=4100 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" rule fuse_bams: @@ -655,7 +655,7 @@ rule htseq_count_reads: log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"), err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err") wrapper: - f"file://{wrappers_dir}/htseq_count_reads" + f"file://{wrappers_dir[0]}/htseq_count_reads" def parse_htseq_counts(counts_filename): @@ -964,7 +964,7 @@ rule compute_RPK: # rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index") # rpk.to_csv(output.rpk_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_RPK" + f"file://{wrappers_dir[0]}/compute_RPK" rule compute_sum_million_RPK: @@ -995,7 +995,7 @@ rule compute_TPM: # tpm = 1000000 * rpk / rpk.sum() # tpm.to_csv(output.tpm_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_TPM" + f"file://{wrappers_dir[0]}/compute_TPM" @wc_applied diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile index 534c17404a4541ea43eb46f6942096520be74322..b749bdb10cfece3fd6a4ff04939b16838e786803 100644 --- a/RNA_Seq_Cecere/RNA-seq.snakefile +++ b/RNA_Seq_Cecere/RNA-seq.snakefile @@ -566,7 +566,7 @@ rule map_on_genome: #shell: # mapping_command(aligner) wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule extract_nomap_polyU: @@ -619,7 +619,7 @@ rule remap_on_genome: #shell: # mapping_command(aligner) wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" def source_sam(wildcards): @@ -659,7 +659,7 @@ rule sam2indexedbam: threads: 8 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" rule compute_mapping_stats: @@ -838,7 +838,7 @@ def biotype2annot(wildcards): # log = OPJ(log_dir, "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"), # err = OPJ(log_dir, "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err"), # wrapper: -# f"file://{wrappers_dir}/htseq_count_reads" +# f"file://{wrappers_dir[0]}/htseq_count_reads" def source_sorted_bam(wildcards): @@ -984,7 +984,7 @@ rule feature_count_reads: # err = OPJ(log_dir, "intersect_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err"), # threads: 4 # to limit memory usage, actually # wrapper: -# f"file://{wrappers_dir}/intersect_count_reads" +# f"file://{wrappers_dir[0]}/intersect_count_reads" rule summarize_counts: @@ -1108,7 +1108,7 @@ rule compute_RPK: # rpk = 1000 * counts_data.loc[common].div(feature_lengths.loc[common]["union_exon_len"], axis="index") # rpk.to_csv(output.rpk_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_RPK" + f"file://{wrappers_dir[0]}/compute_RPK" rule compute_sum_million_RPK: @@ -1143,7 +1143,7 @@ rule compute_TPM: # tpm = 1000000 * rpk / rpk.sum() # tpm.to_csv(output.tpm_file, sep="\t") wrapper: - f"file://{wrappers_dir}/compute_TPM" + f"file://{wrappers_dir[0]}/compute_TPM" # Useful to compute translation efficiency in the Ribo-seq pipeline diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile index 8d45d1555a4772a4e0332c88035d49fa87a0e15b..9a17428ece70455974497f9e0c1c2dc0fbdeb496 100644 --- a/Ribo-seq/Ribo-seq.snakefile +++ b/Ribo-seq/Ribo-seq.snakefile @@ -752,7 +752,7 @@ rule map_on_genome: threads: 4 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" def source_sam(wildcards): @@ -786,7 +786,7 @@ rule sam2indexedbam: resources: mem_mb=4100 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" rule compute_mapping_stats: diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index 8e8c88c8e8d3337e140e31f2720e692aa352bb1f..d7f5e341e53ddf611b02150ab7511248c22b87a0 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -1013,7 +1013,7 @@ rule map_on_genome: resources: mem_mb=700 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" rule extract_nomap_siRNAs: @@ -1066,7 +1066,7 @@ rule remap_on_genome: resources: mem_mb=700 wrapper: - f"file://{wrappers_dir}/map_on_genome" + f"file://{wrappers_dir[0]}/map_on_genome" def source_sam(wildcards): @@ -1101,7 +1101,7 @@ rule sam2indexedbam: resources: mem_mb=4100 wrapper: - f"file://{wrappers_dir}/sam2indexedbam" + f"file://{wrappers_dir[0]}/sam2indexedbam" rule compute_coverage: