Commit 0eb879a8 authored by Blaise Li's avatar Blaise Li
Browse files

Fix path to snakemake wrappers.

parent 0f0690f0
......@@ -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:
......
......@@ -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?
......
......@@ -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
......
......@@ -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
......
......@@ -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:
......
......@@ -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:
......
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