fix: make all scripts executable

CCBR · Oct 16, 2024 · 246825c · 246825c
1 parent 180ba71
commit 246825c
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diff --git a/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py b/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py
diff --git a/workflow/scripts/Create_circExplorer_count_matrix.py b/workflow/scripts/Create_circExplorer_count_matrix.py
diff --git a/workflow/scripts/Create_ciri_count_matrix.py b/workflow/scripts/Create_ciri_count_matrix.py
diff --git a/workflow/scripts/_add_geneid2genepred.py b/workflow/scripts/_add_geneid2genepred.py
diff --git a/workflow/scripts/_append_splice_site_flanks_to_BSJs.py b/workflow/scripts/_append_splice_site_flanks_to_BSJs.py
diff --git a/workflow/scripts/_bam_filter_BSJ_for_HQonly.py b/workflow/scripts/_bam_filter_BSJ_for_HQonly.py
diff --git a/workflow/scripts/_bam_get_alignment_stats.py b/workflow/scripts/_bam_get_alignment_stats.py
diff --git a/workflow/scripts/_bamtobed2readendsbed.py b/workflow/scripts/_bamtobed2readendsbed.py
diff --git a/workflow/scripts/_bedintersect_to_rid2jid.py b/workflow/scripts/_bedintersect_to_rid2jid.py
diff --git a/workflow/scripts/_bedpe2bed.py b/workflow/scripts/_bedpe2bed.py
diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.py b/workflow/scripts/_circExplorer_BSJ_get_strand.py
diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.sh b/workflow/scripts/_circExplorer_BSJ_get_strand.sh
diff --git a/workflow/scripts/_collapse_find_circ.py b/workflow/scripts/_collapse_find_circ.py
diff --git a/workflow/scripts/_compare_lists.py b/workflow/scripts/_compare_lists.py
diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py b/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py
diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_se.py b/workflow/scripts/_create_circExplorer_BSJ_bam_se.py
diff --git a/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py b/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py
diff --git a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
diff --git a/workflow/scripts/_extract_circExplorer_linear_reads.py b/workflow/scripts/_extract_circExplorer_linear_reads.py
diff --git a/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py b/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py
diff --git a/workflow/scripts/_make_master_counts_table.py b/workflow/scripts/_make_master_counts_table.py
diff --git a/workflow/scripts/_make_merge_per_sample_sh.py b/workflow/scripts/_make_merge_per_sample_sh.py
diff --git a/workflow/scripts/_merge_circExplorer_found_counts.py b/workflow/scripts/_merge_circExplorer_found_counts.py
diff --git a/workflow/scripts/_merge_per_sample_counts_table.py b/workflow/scripts/_merge_per_sample_counts_table.py
diff --git a/workflow/scripts/_multifasta2separatefastas.sh b/workflow/scripts/_multifasta2separatefastas.sh
diff --git a/workflow/scripts/_process_bamtobed.py b/workflow/scripts/_process_bamtobed.py
diff --git a/workflow/scripts/_run_circExplorer_bwa.sh b/workflow/scripts/_run_circExplorer_bwa.sh
diff --git a/workflow/scripts/_run_circExplorer_star.sh b/workflow/scripts/_run_circExplorer_star.sh
diff --git a/workflow/scripts/annotate_clear_quant.py b/workflow/scripts/annotate_clear_quant.py
diff --git a/workflow/scripts/apply_junction_filters.py b/workflow/scripts/apply_junction_filters.py
diff --git a/workflow/scripts/bam_get_max_readlen.py b/workflow/scripts/bam_get_max_readlen.py
diff --git a/workflow/scripts/bam_split_by_regions.py b/workflow/scripts/bam_split_by_regions.py
diff --git a/workflow/scripts/bam_to_bigwig.sh b/workflow/scripts/bam_to_bigwig.sh
diff --git a/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py b/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py
diff --git a/workflow/scripts/create_circExplorer_linear_bam.py b/workflow/scripts/create_circExplorer_linear_bam.py
diff --git a/workflow/scripts/create_circExplorer_per_sample_counts_table.py b/workflow/scripts/create_circExplorer_per_sample_counts_table.py
diff --git a/workflow/scripts/create_dcc_per_sample_counts_table.py b/workflow/scripts/create_dcc_per_sample_counts_table.py
diff --git a/workflow/scripts/create_mapsplice_per_sample_counts_table.py b/workflow/scripts/create_mapsplice_per_sample_counts_table.py
diff --git a/workflow/scripts/create_nclscan_per_sample_counts_table.py b/workflow/scripts/create_nclscan_per_sample_counts_table.py
diff --git a/workflow/scripts/filter_bam.py b/workflow/scripts/filter_bam.py
diff --git a/workflow/scripts/filter_bam_by_readids.py b/workflow/scripts/filter_bam_by_readids.py
diff --git a/workflow/scripts/filter_bam_for_BSJs.py b/workflow/scripts/filter_bam_for_BSJs.py
diff --git a/workflow/scripts/filter_bam_for_linear_reads.py b/workflow/scripts/filter_bam_for_linear_reads.py
diff --git a/workflow/scripts/filter_bam_for_splice_reads.py b/workflow/scripts/filter_bam_for_splice_reads.py
diff --git a/workflow/scripts/filter_dcc.py b/workflow/scripts/filter_dcc.py
diff --git a/workflow/scripts/filter_junction.py b/workflow/scripts/filter_junction.py
diff --git a/workflow/scripts/filter_junction_human.py b/workflow/scripts/filter_junction_human.py
diff --git a/workflow/scripts/fix_gtfs.py b/workflow/scripts/fix_gtfs.py
diff --git a/workflow/scripts/fix_refseq_gtf.py b/workflow/scripts/fix_refseq_gtf.py
diff --git a/workflow/scripts/gather_cluster_stats.sh b/workflow/scripts/gather_cluster_stats.sh
diff --git a/workflow/scripts/get_index_rl.py b/workflow/scripts/get_index_rl.py
diff --git a/workflow/scripts/junctions2readids.py b/workflow/scripts/junctions2readids.py
diff --git a/workflow/scripts/make_star_index.sh b/workflow/scripts/make_star_index.sh
diff --git a/workflow/scripts/merge_ReadsPerGene_counts.R b/workflow/scripts/merge_ReadsPerGene_counts.R
diff --git a/workflow/scripts/merge_counts_tables_2_counts_matrix.py b/workflow/scripts/merge_counts_tables_2_counts_matrix.py
diff --git a/workflow/scripts/reformat_hg38_2_hg19.py b/workflow/scripts/reformat_hg38_2_hg19.py
diff --git a/workflow/scripts/transcript2gene.py b/workflow/scripts/transcript2gene.py
diff --git a/workflow/scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py b/workflow/scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py
diff --git a/workflow/scripts/venn.R b/workflow/scripts/venn.R