diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile index 8e12e5bcf22100c0d2e1b7a7390970a69ea64fcc..bca5c259b734c27e1530a26323819475054990a9 100644 --- a/PRO-seq/PRO-seq.snakefile +++ b/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: diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile index 6f9b41901e0529193442477022395b851b89fbd3..9263c50a6f85f33c636e1c509f6a5987fce53d69 100644 --- a/RNA_Seq_Cecere/RNA-seq.snakefile +++ b/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: diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile index 8d45d1555a4772a4e0332c88035d49fa87a0e15b..fe47b8bc1ff8c45a423205d50081ed96f21d5326 100644 --- a/Ribo-seq/Ribo-seq.snakefile +++ b/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: diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt index 7d1c2447c473a99eebb0559a62674f2c87d6e39c..6e99775ef7f45f9d971ce9358ca2c75b6cc0254e 100644 --- a/small_RNA-seq/requirements.txt +++ b/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 diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index 8e8c88c8e8d3337e140e31f2720e692aa352bb1f..889c3c85c23c43bbefc813e16bfed77dd7fba670 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/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: