Fix path to snakemake wrappers.

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:

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?

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

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

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:

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: