.gitignore
LICENSE
MANIFEST.in
README.md
environment.yml
project_file.yaml
rocketchip-environment.yml
rocketchip_flowchart.png
setup.cfg
setup.py
conda-recipe/bld.bat
conda-recipe/meta.yaml
rocketchip.egg-info/PKG-INFO
rocketchip.egg-info/SOURCES.txt
rocketchip.egg-info/dependency_links.txt
rocketchip.egg-info/entry_points.txt
rocketchip.egg-info/requires.txt
rocketchip.egg-info/top_level.txt
rocketchip_pkg/__init__.py
rocketchip_pkg/rocketchip.py
rocketchip_pkg/rules/align_reads/STAR_paired.txt
rocketchip_pkg/rules/align_reads/STAR_single.txt
rocketchip_pkg/rules/align_reads/bowtie2_paired.txt
rocketchip_pkg/rules/align_reads/bowtie2_single.txt
rocketchip_pkg/rules/align_reads/bwa_mem_paired.txt
rocketchip_pkg/rules/align_reads/bwa_mem_single.txt
rocketchip_pkg/rules/bam_to_bigwig/bam_to_bigwig.txt
rocketchip_pkg/rules/call_peaks/cisgenome/cisgenome_no_control.txt
rocketchip_pkg/rules/call_peaks/cisgenome/cisgenome_with_control.txt
rocketchip_pkg/rules/call_peaks/genrich/genrich_no_control.txt
rocketchip_pkg/rules/call_peaks/genrich/genrich_with_control.txt
rocketchip_pkg/rules/call_peaks/macs3/macs3_no_control.txt
rocketchip_pkg/rules/call_peaks/macs3/macs3_with_control.txt
rocketchip_pkg/rules/call_peaks/peakseq/peakseq_with_control.txt
rocketchip_pkg/rules/call_peaks/pepr/pepr_with_control.txt
rocketchip_pkg/rules/evaluate_peaks/evals.txt
rocketchip_pkg/rules/fastqc/postprocessing_paired.txt
rocketchip_pkg/rules/fastqc/postprocessing_single.txt
rocketchip_pkg/rules/fastqc/preprocessing_paired.txt
rocketchip_pkg/rules/fastqc/preprocessing_single.txt
rocketchip_pkg/rules/get_genome/local_genome.txt
rocketchip_pkg/rules/get_genome/remote_fa_gz_genome.txt
rocketchip_pkg/rules/get_genome/remote_hg38_genome.txt
rocketchip_pkg/rules/get_genome/remote_tar_gz_genome.txt
rocketchip_pkg/rules/get_reads/local_reads_paired.txt
rocketchip_pkg/rules/get_reads/local_reads_single.txt
rocketchip_pkg/rules/get_reads/remote_reads_paired.txt
rocketchip_pkg/rules/get_reads/remote_reads_single.txt
rocketchip_pkg/rules/index_genome/STAR.txt
rocketchip_pkg/rules/index_genome/bowtie2.txt
rocketchip_pkg/rules/index_genome/bwa_mem.txt
rocketchip_pkg/rules/make_dir/make_dir.txt
rocketchip_pkg/rules/mark_dup/fake_dedup.txt
rocketchip_pkg/rules/mark_dup/picard_dedup.txt
rocketchip_pkg/rules/mark_dup/sambamba_dedup.txt
rocketchip_pkg/rules/mark_dup/samtools_dedup.txt
rocketchip_pkg/rules/parse_reads/parse_reads_no_control.txt
rocketchip_pkg/rules/parse_reads/parse_reads_with_control.txt
rocketchip_pkg/rules/rule_all/bigwig/bigwig.txt
rocketchip_pkg/rules/rule_all/fastq/fastq_no_control_paired.txt
rocketchip_pkg/rules/rule_all/fastq/fastq_no_control_single.txt
rocketchip_pkg/rules/rule_all/fastq/fastq_with_control_paired.txt
rocketchip_pkg/rules/rule_all/fastq/fastq_with_control_single.txt
rocketchip_pkg/rules/rule_all/peaks/cisgenome_no_control.txt
rocketchip_pkg/rules/rule_all/peaks/cisgenome_with_control.txt
rocketchip_pkg/rules/rule_all/peaks/genrich_no_control.txt
rocketchip_pkg/rules/rule_all/peaks/genrich_with_control.txt
rocketchip_pkg/rules/rule_all/peaks/macs3_no_control.txt
rocketchip_pkg/rules/rule_all/peaks/macs3_with_control.txt
rocketchip_pkg/rules/rule_all/peaks/peakseq_with_control.txt
rocketchip_pkg/rules/rule_all/peaks/pepr_with_control.txt
rocketchip_pkg/rules/sort_index_reads/samtools_index.txt
rocketchip_pkg/rules/sort_index_reads/samtools_sort.txt
rocketchip_pkg/tests/functional_test.py
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/exp_a_1.fastq.gz
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/exp_a_2.fastq.gz
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/exp_b_1.fastq.gz
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/exp_b_2.fastq.gz
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/genome.fa
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/input_1.fastq.gz
rocketchip_pkg/tests/seq_data/paired_narrow/test_1/input_2.fastq.gz
rocketchip_pkg/tools/chrominfo
rocketchip_pkg/tools/readfasta.py
rocketchip_pkg/tools/sam2aln
rocketchip_pkg/tools/scrape_sras.py