From 246825cc623dae8735a87276ba480d82b3e87c4a Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 16 Oct 2024 15:35:46 -0400 Subject: [PATCH] fix: make all scripts executable --- workflow/scripts/Create_circExplorer_BSJ_count_matrix.py | 0 workflow/scripts/Create_circExplorer_count_matrix.py | 0 workflow/scripts/Create_ciri_count_matrix.py | 0 workflow/scripts/_add_geneid2genepred.py | 0 workflow/scripts/_append_splice_site_flanks_to_BSJs.py | 0 workflow/scripts/_bam_filter_BSJ_for_HQonly.py | 0 workflow/scripts/_bam_get_alignment_stats.py | 0 workflow/scripts/_bamtobed2readendsbed.py | 0 workflow/scripts/_bedintersect_to_rid2jid.py | 0 workflow/scripts/_bedpe2bed.py | 0 workflow/scripts/_circExplorer_BSJ_get_strand.py | 0 workflow/scripts/_circExplorer_BSJ_get_strand.sh | 0 workflow/scripts/_collapse_find_circ.py | 0 workflow/scripts/_compare_lists.py | 0 workflow/scripts/_create_circExplorer_BSJ_bam_pe.py | 0 workflow/scripts/_create_circExplorer_BSJ_bam_se.py | 0 workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py | 0 workflow/scripts/_create_circExplorer_linear_bam.v2.sh | 0 workflow/scripts/_extract_circExplorer_linear_reads.py | 0 workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py | 0 workflow/scripts/_make_master_counts_table.py | 0 workflow/scripts/_make_merge_per_sample_sh.py | 0 workflow/scripts/_merge_circExplorer_found_counts.py | 0 workflow/scripts/_merge_per_sample_counts_table.py | 0 workflow/scripts/_multifasta2separatefastas.sh | 0 workflow/scripts/_process_bamtobed.py | 0 workflow/scripts/_run_circExplorer_bwa.sh | 0 workflow/scripts/_run_circExplorer_star.sh | 0 workflow/scripts/annotate_clear_quant.py | 0 workflow/scripts/apply_junction_filters.py | 0 workflow/scripts/bam_get_max_readlen.py | 0 workflow/scripts/bam_split_by_regions.py | 0 workflow/scripts/bam_to_bigwig.sh | 0 workflow/scripts/circExplorer_get_annotated_counts_per_sample.py | 0 workflow/scripts/create_circExplorer_linear_bam.py | 0 workflow/scripts/create_circExplorer_per_sample_counts_table.py | 0 workflow/scripts/create_dcc_per_sample_counts_table.py | 0 workflow/scripts/create_mapsplice_per_sample_counts_table.py | 0 workflow/scripts/create_nclscan_per_sample_counts_table.py | 0 workflow/scripts/filter_bam.py | 0 workflow/scripts/filter_bam_by_readids.py | 0 workflow/scripts/filter_bam_for_BSJs.py | 0 workflow/scripts/filter_bam_for_linear_reads.py | 0 workflow/scripts/filter_bam_for_splice_reads.py | 0 workflow/scripts/filter_dcc.py | 0 workflow/scripts/filter_junction.py | 0 workflow/scripts/filter_junction_human.py | 0 workflow/scripts/fix_gtfs.py | 0 workflow/scripts/fix_refseq_gtf.py | 0 workflow/scripts/gather_cluster_stats.sh | 0 workflow/scripts/get_index_rl.py | 0 workflow/scripts/junctions2readids.py | 0 workflow/scripts/make_star_index.sh | 0 workflow/scripts/merge_ReadsPerGene_counts.R | 0 workflow/scripts/merge_counts_tables_2_counts_matrix.py | 0 workflow/scripts/reformat_hg38_2_hg19.py | 0 workflow/scripts/transcript2gene.py | 0 .../scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py | 0 workflow/scripts/venn.R | 0 59 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 workflow/scripts/Create_circExplorer_BSJ_count_matrix.py mode change 100644 => 100755 workflow/scripts/Create_circExplorer_count_matrix.py mode change 100644 => 100755 workflow/scripts/Create_ciri_count_matrix.py mode change 100644 => 100755 workflow/scripts/_add_geneid2genepred.py mode change 100644 => 100755 workflow/scripts/_append_splice_site_flanks_to_BSJs.py mode change 100644 => 100755 workflow/scripts/_bam_filter_BSJ_for_HQonly.py mode change 100644 => 100755 workflow/scripts/_bam_get_alignment_stats.py mode change 100644 => 100755 workflow/scripts/_bamtobed2readendsbed.py mode change 100644 => 100755 workflow/scripts/_bedintersect_to_rid2jid.py mode change 100644 => 100755 workflow/scripts/_bedpe2bed.py mode change 100644 => 100755 workflow/scripts/_circExplorer_BSJ_get_strand.py mode change 100644 => 100755 workflow/scripts/_circExplorer_BSJ_get_strand.sh mode change 100644 => 100755 workflow/scripts/_collapse_find_circ.py mode change 100644 => 100755 workflow/scripts/_compare_lists.py mode change 100644 => 100755 workflow/scripts/_create_circExplorer_BSJ_bam_pe.py mode change 100644 => 100755 workflow/scripts/_create_circExplorer_BSJ_bam_se.py mode change 100644 => 100755 workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py mode change 100644 => 100755 workflow/scripts/_create_circExplorer_linear_bam.v2.sh mode change 100644 => 100755 workflow/scripts/_extract_circExplorer_linear_reads.py mode change 100644 => 100755 workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py mode change 100644 => 100755 workflow/scripts/_make_master_counts_table.py mode change 100644 => 100755 workflow/scripts/_make_merge_per_sample_sh.py mode change 100644 => 100755 workflow/scripts/_merge_circExplorer_found_counts.py mode change 100644 => 100755 workflow/scripts/_merge_per_sample_counts_table.py mode change 100644 => 100755 workflow/scripts/_multifasta2separatefastas.sh mode change 100644 => 100755 workflow/scripts/_process_bamtobed.py mode change 100644 => 100755 workflow/scripts/_run_circExplorer_bwa.sh mode change 100644 => 100755 workflow/scripts/_run_circExplorer_star.sh mode change 100644 => 100755 workflow/scripts/annotate_clear_quant.py mode change 100644 => 100755 workflow/scripts/apply_junction_filters.py mode change 100644 => 100755 workflow/scripts/bam_get_max_readlen.py mode change 100644 => 100755 workflow/scripts/bam_split_by_regions.py mode change 100644 => 100755 workflow/scripts/bam_to_bigwig.sh mode change 100644 => 100755 workflow/scripts/circExplorer_get_annotated_counts_per_sample.py mode change 100644 => 100755 workflow/scripts/create_circExplorer_linear_bam.py mode change 100644 => 100755 workflow/scripts/create_circExplorer_per_sample_counts_table.py mode change 100644 => 100755 workflow/scripts/create_dcc_per_sample_counts_table.py mode change 100644 => 100755 workflow/scripts/create_mapsplice_per_sample_counts_table.py mode change 100644 => 100755 workflow/scripts/create_nclscan_per_sample_counts_table.py mode change 100644 => 100755 workflow/scripts/filter_bam.py mode change 100644 => 100755 workflow/scripts/filter_bam_by_readids.py mode change 100644 => 100755 workflow/scripts/filter_bam_for_BSJs.py mode change 100644 => 100755 workflow/scripts/filter_bam_for_linear_reads.py mode change 100644 => 100755 workflow/scripts/filter_bam_for_splice_reads.py mode change 100644 => 100755 workflow/scripts/filter_dcc.py mode change 100644 => 100755 workflow/scripts/filter_junction.py mode change 100644 => 100755 workflow/scripts/filter_junction_human.py mode change 100644 => 100755 workflow/scripts/fix_gtfs.py mode change 100644 => 100755 workflow/scripts/fix_refseq_gtf.py mode change 100644 => 100755 workflow/scripts/gather_cluster_stats.sh mode change 100644 => 100755 workflow/scripts/get_index_rl.py mode change 100644 => 100755 workflow/scripts/junctions2readids.py mode change 100644 => 100755 workflow/scripts/make_star_index.sh mode change 100644 => 100755 workflow/scripts/merge_ReadsPerGene_counts.R mode change 100644 => 100755 workflow/scripts/merge_counts_tables_2_counts_matrix.py mode change 100644 => 100755 workflow/scripts/reformat_hg38_2_hg19.py mode change 100644 => 100755 workflow/scripts/transcript2gene.py mode change 100644 => 100755 workflow/scripts/validate_BSJ_reads_and_split_BSJ_bam_by_strand.py mode change 100644 => 100755 workflow/scripts/venn.R diff --git a/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py b/workflow/scripts/Create_circExplorer_BSJ_count_matrix.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/Create_circExplorer_count_matrix.py b/workflow/scripts/Create_circExplorer_count_matrix.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/Create_ciri_count_matrix.py b/workflow/scripts/Create_ciri_count_matrix.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_add_geneid2genepred.py b/workflow/scripts/_add_geneid2genepred.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_append_splice_site_flanks_to_BSJs.py b/workflow/scripts/_append_splice_site_flanks_to_BSJs.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_bam_filter_BSJ_for_HQonly.py b/workflow/scripts/_bam_filter_BSJ_for_HQonly.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_bam_get_alignment_stats.py b/workflow/scripts/_bam_get_alignment_stats.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_bamtobed2readendsbed.py b/workflow/scripts/_bamtobed2readendsbed.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_bedintersect_to_rid2jid.py b/workflow/scripts/_bedintersect_to_rid2jid.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_bedpe2bed.py b/workflow/scripts/_bedpe2bed.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.py b/workflow/scripts/_circExplorer_BSJ_get_strand.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_circExplorer_BSJ_get_strand.sh b/workflow/scripts/_circExplorer_BSJ_get_strand.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/_collapse_find_circ.py b/workflow/scripts/_collapse_find_circ.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_compare_lists.py b/workflow/scripts/_compare_lists.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py b/workflow/scripts/_create_circExplorer_BSJ_bam_pe.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_create_circExplorer_BSJ_bam_se.py b/workflow/scripts/_create_circExplorer_BSJ_bam_se.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py b/workflow/scripts/_create_circExplorer_BSJ_hqonly_pe.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/_extract_circExplorer_linear_reads.py b/workflow/scripts/_extract_circExplorer_linear_reads.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py b/workflow/scripts/_filter_linear_spliced_readids_w_rid2jid.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_make_master_counts_table.py b/workflow/scripts/_make_master_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_make_merge_per_sample_sh.py b/workflow/scripts/_make_merge_per_sample_sh.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_merge_circExplorer_found_counts.py b/workflow/scripts/_merge_circExplorer_found_counts.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_merge_per_sample_counts_table.py b/workflow/scripts/_merge_per_sample_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_multifasta2separatefastas.sh b/workflow/scripts/_multifasta2separatefastas.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/_process_bamtobed.py b/workflow/scripts/_process_bamtobed.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/_run_circExplorer_bwa.sh b/workflow/scripts/_run_circExplorer_bwa.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/_run_circExplorer_star.sh b/workflow/scripts/_run_circExplorer_star.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/annotate_clear_quant.py b/workflow/scripts/annotate_clear_quant.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/apply_junction_filters.py b/workflow/scripts/apply_junction_filters.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/bam_get_max_readlen.py b/workflow/scripts/bam_get_max_readlen.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/bam_split_by_regions.py b/workflow/scripts/bam_split_by_regions.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/bam_to_bigwig.sh b/workflow/scripts/bam_to_bigwig.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py b/workflow/scripts/circExplorer_get_annotated_counts_per_sample.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/create_circExplorer_linear_bam.py b/workflow/scripts/create_circExplorer_linear_bam.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/create_circExplorer_per_sample_counts_table.py b/workflow/scripts/create_circExplorer_per_sample_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/create_dcc_per_sample_counts_table.py b/workflow/scripts/create_dcc_per_sample_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/create_mapsplice_per_sample_counts_table.py b/workflow/scripts/create_mapsplice_per_sample_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/create_nclscan_per_sample_counts_table.py b/workflow/scripts/create_nclscan_per_sample_counts_table.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_bam.py b/workflow/scripts/filter_bam.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_bam_by_readids.py b/workflow/scripts/filter_bam_by_readids.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_bam_for_BSJs.py b/workflow/scripts/filter_bam_for_BSJs.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_bam_for_linear_reads.py b/workflow/scripts/filter_bam_for_linear_reads.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_bam_for_splice_reads.py b/workflow/scripts/filter_bam_for_splice_reads.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_dcc.py b/workflow/scripts/filter_dcc.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_junction.py b/workflow/scripts/filter_junction.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/filter_junction_human.py b/workflow/scripts/filter_junction_human.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/fix_gtfs.py b/workflow/scripts/fix_gtfs.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/fix_refseq_gtf.py b/workflow/scripts/fix_refseq_gtf.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/gather_cluster_stats.sh b/workflow/scripts/gather_cluster_stats.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/get_index_rl.py b/workflow/scripts/get_index_rl.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/junctions2readids.py b/workflow/scripts/junctions2readids.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/make_star_index.sh b/workflow/scripts/make_star_index.sh old mode 100644 new mode 100755 diff --git a/workflow/scripts/merge_ReadsPerGene_counts.R b/workflow/scripts/merge_ReadsPerGene_counts.R old mode 100644 new mode 100755 diff --git a/workflow/scripts/merge_counts_tables_2_counts_matrix.py b/workflow/scripts/merge_counts_tables_2_counts_matrix.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/reformat_hg38_2_hg19.py b/workflow/scripts/reformat_hg38_2_hg19.py old mode 100644 new mode 100755 diff --git a/workflow/scripts/transcript2gene.py b/workflow/scripts/transcript2gene.py old mode 100644 new mode 100755 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 old mode 100644 new mode 100755 diff --git a/workflow/scripts/venn.R b/workflow/scripts/venn.R old mode 100644 new mode 100755