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kraken.rules version 1.0 and 1.1 ./bam_analysis/bam_analysis.rules ./bam_quality_filter/bam_quality_filter.rules ./bed_to_gff/bed_to_gff.rules ./bwa_bam_to_fastq/bwa_bam_to_fastq.rules ./codecs/bam_to_fasta/bam_to_fasta.rules ./codecs/bz2_to_dsrc/bz2_to_dsrc.rules ./codecs/bz2_to_fastq/bz2_to_fastq.rules ./codecs/dsrc_to_bz2/dsrc_to_bz2.rules ./codecs/dsrc_to_fastq/dsrc_to_fastq.rules ./codecs/fastq_to_bz2/fastq_to_bz2.rules ./codecs/fastq_to_dsrc/fastq_to_dsrc.rules ./codecs/fastq_to_gz/fastq_to_gz.rules ./codecs/gz_to_dsrc/gz_to_dsrc.rules ./codecs/gz_to_fastq/gz_to_fastq.rules ./copy_multiple_files/copy_multiple_files.rules ./deeptools/BamPEFragmentSize/BamPEFragmentSize.rules ./deeptools/multiBamSummary/multiBamSummary.rules ./deeptools/plotCorrelation/plotCorrelation.rules ./deeptools/plotCoverage/plotCoverage.rules ./digital_normalisation/digital_normalisation.rules ./DupRadar/DupRadar.rules ./extract_fasta_from_bed/extract_fasta_from_bed.rules ./fastq_sampling/fastq_sampling.rules ./fastq_screen/fastq_screen.rules ./fastq_screen_report/fastq_screen_report.rules ./format_contigs/format_contigs.rules ./idr/compute_idr/compute_idr.rules ./idr/intersectionApproach/intersectionApproach.rules ./idr/metrics_peaks/metrics_peaks.rules ./idr/preIDR_dynamic/preIDR_dynamic.rules ./idr/select_peaks/select_peaks.rules ./idr/stats_peakCalling/stats_peakCalling.rules ./idr/union_peaks/union_peaks.rules ./igvtools/igvtools.rules ./indel_realigner/indel_realigner.rules ./kraken/2.0/kraken.rules ./mapping_analysis/mapping_analysis.rules ./miRNA_count_dynamic/miRNA_count_dynamic.rules ./pacbio_quality/pacbio_quality.rules ./picard-tools/CollectInsertSizeMetrics/CollectInsertSizeMetrics.rules ./picard-tools/create_sequence_dictionary/create_sequence_dictionary.rules ./picard-tools/mark_duplicates_dynamic/mark_duplicates_dynamic.rules ./picard-tools/reorderSam/reorderSam.rules ./preSARTools/preSARTools.rules ./prokka/prokka.rules ./quast/quast.rules ./remove_blacklist/remove_blacklist.rules ./revcomp_rule/revcomp_rule.rules ./rnaseqc/rnaseqc.rules ./samtools_sort/samtools_sort.rules ./SARTools/SARTools.rules ./SnpEff/snpeff_create_database/snpeff_create_database.rules ./spikes_counting/spikes_counting.rules ./spp/spp.rules ./summary_pipeline/summary_pipeline.rules ./tophat_mapping/tophat_mapping.rules ./Variant_caller/freebayes_bcf_filter/freebayes_bcf_filter.rules
The text was updated successfully, but these errors were encountered:
No branches or pull requests
Needed in pipelines
not needed / deprecated / to be removed
To do
kraken.rules version 1.0 and 1.1
./bam_analysis/bam_analysis.rules
./bam_quality_filter/bam_quality_filter.rules
./bed_to_gff/bed_to_gff.rules
./bwa_bam_to_fastq/bwa_bam_to_fastq.rules
./codecs/bam_to_fasta/bam_to_fasta.rules
./codecs/bz2_to_dsrc/bz2_to_dsrc.rules
./codecs/bz2_to_fastq/bz2_to_fastq.rules
./codecs/dsrc_to_bz2/dsrc_to_bz2.rules
./codecs/dsrc_to_fastq/dsrc_to_fastq.rules
./codecs/fastq_to_bz2/fastq_to_bz2.rules
./codecs/fastq_to_dsrc/fastq_to_dsrc.rules
./codecs/fastq_to_gz/fastq_to_gz.rules
./codecs/gz_to_dsrc/gz_to_dsrc.rules
./codecs/gz_to_fastq/gz_to_fastq.rules
./copy_multiple_files/copy_multiple_files.rules
./deeptools/BamPEFragmentSize/BamPEFragmentSize.rules
./deeptools/multiBamSummary/multiBamSummary.rules
./deeptools/plotCorrelation/plotCorrelation.rules
./deeptools/plotCoverage/plotCoverage.rules
./digital_normalisation/digital_normalisation.rules
./DupRadar/DupRadar.rules
./extract_fasta_from_bed/extract_fasta_from_bed.rules
./fastq_sampling/fastq_sampling.rules
./fastq_screen/fastq_screen.rules
./fastq_screen_report/fastq_screen_report.rules
./format_contigs/format_contigs.rules
./idr/compute_idr/compute_idr.rules
./idr/intersectionApproach/intersectionApproach.rules
./idr/metrics_peaks/metrics_peaks.rules
./idr/preIDR_dynamic/preIDR_dynamic.rules
./idr/select_peaks/select_peaks.rules
./idr/stats_peakCalling/stats_peakCalling.rules
./idr/union_peaks/union_peaks.rules
./igvtools/igvtools.rules
./indel_realigner/indel_realigner.rules
./kraken/2.0/kraken.rules
./mapping_analysis/mapping_analysis.rules
./miRNA_count_dynamic/miRNA_count_dynamic.rules
./pacbio_quality/pacbio_quality.rules
./picard-tools/CollectInsertSizeMetrics/CollectInsertSizeMetrics.rules
./picard-tools/create_sequence_dictionary/create_sequence_dictionary.rules
./picard-tools/mark_duplicates_dynamic/mark_duplicates_dynamic.rules
./picard-tools/reorderSam/reorderSam.rules
./preSARTools/preSARTools.rules
./prokka/prokka.rules
./quast/quast.rules
./remove_blacklist/remove_blacklist.rules
./revcomp_rule/revcomp_rule.rules
./rnaseqc/rnaseqc.rules
./samtools_sort/samtools_sort.rules
./SARTools/SARTools.rules
./SnpEff/snpeff_create_database/snpeff_create_database.rules
./spikes_counting/spikes_counting.rules
./spp/spp.rules
./summary_pipeline/summary_pipeline.rules
./tophat_mapping/tophat_mapping.rules
./Variant_caller/freebayes_bcf_filter/freebayes_bcf_filter.rules
The text was updated successfully, but these errors were encountered: