Reverting snakefiles to use plain wrappers_dir.

e10a0af2 · Blaise Li · 182bef09 · e10a0af2 · e10a0af2 · e10a0af2
Commit e10a0af2 authored Oct 30, 2019 by Blaise Li
--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 rule sam2indexedbam:
@@ -474,7 +474,7 @@ rule sam2indexedbam:
    resources:
        mem_mb=4100
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/sam2indexedbam"


 rule compute_mapping_stats:

--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 rule sam2indexedbam:
@@ -189,7 +189,7 @@ rule sam2indexedbam:
    resources:
        mem_mb=4100
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/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[0]}/compute_RPK"
+        f"file://{wrappers_dir}/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[0]}/compute_TPM"
+        f"file://{wrappers_dir}/compute_TPM"


 # TODO: Is it better to compute the mean and then the fold of the means?

--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 rule sam2indexedbam:
@@ -510,7 +510,7 @@ rule sam2indexedbam:
    resources:
        mem_mb=4100
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/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[0]}/htseq_count_reads"
+        f"file://{wrappers_dir}/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[0]}/compute_RPK"
+        f"file://{wrappers_dir}/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[0]}/compute_TPM"
+        f"file://{wrappers_dir}/compute_TPM"


 @wc_applied

--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 rule extract_nomap_polyU:
@@ -619,7 +619,7 @@ rule remap_on_genome:
    #shell:
    #    mapping_command(aligner)
    wrapper:
-        f"file://{wrappers_dir[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 def source_sam(wildcards):
@@ -659,7 +659,7 @@ rule sam2indexedbam:
    threads:
        8
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/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[0]}/htseq_count_reads"
+#         f"file://{wrappers_dir}/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[0]}/intersect_count_reads"
+#         f"file://{wrappers_dir}/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[0]}/compute_RPK"
+        f"file://{wrappers_dir}/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[0]}/compute_TPM"
+        f"file://{wrappers_dir}/compute_TPM"


 # Useful to compute translation efficiency in the Ribo-seq pipeline

--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 def source_sam(wildcards):
@@ -786,7 +786,7 @@ rule sam2indexedbam:
    resources:
        mem_mb=4100
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/sam2indexedbam"


 rule compute_mapping_stats:

--- 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[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 rule extract_nomap_siRNAs:
@@ -1066,7 +1066,7 @@ rule remap_on_genome:
    resources:
        mem_mb=700
    wrapper:
-        f"file://{wrappers_dir[0]}/map_on_genome"
+        f"file://{wrappers_dir}/map_on_genome"


 def source_sam(wildcards):
@@ -1101,7 +1101,7 @@ rule sam2indexedbam:
    resources:
        mem_mb=4100
    wrapper:
-        f"file://{wrappers_dir[0]}/sam2indexedbam"
+        f"file://{wrappers_dir}/sam2indexedbam"


 rule compute_coverage: