Workaround check added in pyBigWig.

See https://github.com/deeptools/pyBigWig/issues/97

PRO-seq/PRO-seq.snakefile

@@ -1179,7 +1179,7 @@ rule merge_bigwig_reps:
             else:
                 bw_out = pyBigWig.open(output.bw, "w")
                 bw_out.addHeader(list(chrom_sizes.items()))
-                for (chrom, chrom_len) in bw_out.chroms().items():
+                for (chrom, chrom_len) in chrom_sizes.items():
                     try:
                         assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
                     except KeyError as e:

RNA_Seq_Cecere/RNA-seq.snakefile

@@ -1486,7 +1486,7 @@ rule merge_bigwig_reps:
             else:
                 bw_out = pyBigWig.open(output.bw, "w")
                 bw_out.addHeader(list(chrom_sizes.items()))
-                for (chrom, chrom_len) in bw_out.chroms().items():
+                for (chrom, chrom_len) in chrom_sizes.items():
                     try:
                         assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
                     except KeyError as e:

Ribo-seq/Ribo-seq.snakefile

@@ -1850,7 +1850,7 @@ rule merge_bigwig_reps:
             else:
                 bw_out = pyBigWig.open(output.bw, "w")
                 bw_out.addHeader(list(chrom_sizes.items()))
-                for (chrom, chrom_len) in bw_out.chroms().items():
+                for (chrom, chrom_len) in chrom_sizes.items():
                     try:
                         assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
                     except KeyError as e:

small_RNA-seq/requirements.txt

@@ -14,7 +14,6 @@ libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/li
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
 rpy2
-
 # extra dependencies for the sRNA-seq annotation script small_RNA_seq_annotate.py
 pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
 pysam

small_RNA-seq/small_RNA-seq.snakefile

@@ -2772,7 +2772,7 @@ rule merge_bigwig_reps:
             else:
                 bw_out = pyBigWig.open(output.bw, "w")
                 bw_out.addHeader(list(chrom_sizes.items()))
-                for (chrom, chrom_len) in bw_out.chroms().items():
+                for (chrom, chrom_len) in chrom_sizes.items():
                     try:
                         assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
                     except KeyError as e: