No PCA when only one library.

Also updated one gene list name.

PRO-seq/PRO-seq.snakefile

@@ -169,7 +169,7 @@ ID_LISTS = [
     "germline_specific",
     "histone",
     "spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014",
-    "piRNA_dependent_prot_si_down4_WR_RT_top200", "piRNA_dependent_prot_si_down4",
+    "piRNA_dependent_prot_si_down4_WR_RT_top200", "piRNA_dependent_prot_si_22G_down4",
     "csr1_prot_si_supertargets_common"]
 annot_dir = config["annot_dir"]
 gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
@@ -287,6 +287,14 @@ wildcard_constraints:
 # Define functions to be used in shell portions
 shell.prefix(SHELL_FUNCTIONS)
 
+if len(CONDITIONS) < 2:
+    pca_figs = []
+else:
+    pca_figs = expand(OPJ(
+        output_dir, "{trimmer}", "figures", aligner, "{counter}",
+        "{biotype}_{orientation}_PCA.pdf"),
+        trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
+        orientation=ORIENTATIONS),
 
 rule all:
     """This top rule is used to drive the whole workflow by taking as input its final products."""
@@ -306,11 +314,12 @@ rule all:
             "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.pdf"),
-            trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
-            orientation=ORIENTATIONS),
+        pca_figs,
+        #expand(OPJ(
+        #    output_dir, "{trimmer}", "figures", aligner, "{counter}",
+        #    "{biotype}_{orientation}_PCA.pdf"),
+        #    trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES,
+        #    orientation=ORIENTATIONS),
         #expand(OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"), trimmer=TRIMMERS, counter=COUNTERS, orientation=["all"]),
         #expand(expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "{lib}_{rep}_on_C_elegans", "{{biotype}}_{{orientation}}_counts.txt"), filtered_product, lib=LIBS, rep=REPS), trimmer=TRIMMERS, counter=COUNTERS, biotype=COUNT_BIOTYPES, orientation=["all"]),
         expand(expand(OPJ(