Commit 49cfaa10 authored by Blaise Li's avatar Blaise Li
Browse files

Reactivate lfc distribution plots in GRO-seq.

parent 6490b085
......@@ -244,7 +244,7 @@ rule all:
"""This top rule is used to drive the whole workflow by taking as input its final products."""
input:
expand(OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{contrast}", "{orientation}_{biotype}", "MA_with_{id_list}.pdf"), trimmer=TRIMMERS, counter=COUNTERS, contrast=CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES, id_list=ID_LISTS),
#expand(OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{contrast}", "{orientation}_{biotype}_{fold_type}_distribution.pdf"), trimmer=TRIMMERS, counter=COUNTERS, contrast=CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES, fold_type=["log2FoldChange"]),
expand(OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{contrast}", "{orientation}_{biotype}", "{fold_type}_distribution.pdf"), trimmer=TRIMMERS, counter=COUNTERS, contrast=CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES, fold_type=["log2FoldChange"]),
expand(OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "deseq2", "{contrast}", "{orientation}_{biotype}", "counts_and_res.txt"), trimmer=TRIMMERS, counter=COUNTERS, contrast=CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES),
expand(OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{biotype}_{orientation}_PCA.{fig_format}"), trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES, orientation=ORIENTATIONS, fig_format=FIG_FORMATS),
#expand(OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"), trimmer=TRIMMERS, counter=COUNTERS, orientation=["all"]),
......@@ -1116,7 +1116,7 @@ rule make_lfc_distrib_plot:
input:
deseq_results = rules.differential_expression.output.deseq_results,
output:
lfc_plot = OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{contrast}", "{orientation}_{biotype}_{fold_type}_distribution.pdf"),
lfc_plot = OPJ(output_dir, "{trimmer}", "figures", aligner, "{counter}", "{contrast}", "{orientation}_{biotype}", "{fold_type}_distribution.pdf"),
run:
if test_na_file(input.deseq_results):
warnings.warn(
......
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