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rules from sequana to integrate (possibly) #12

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cokelaer opened this issue Aug 10, 2021 · 0 comments
Open
3 tasks

rules from sequana to integrate (possibly) #12

cokelaer opened this issue Aug 10, 2021 · 0 comments

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@cokelaer
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cokelaer commented Aug 10, 2021

name wrapper doc sequana rule using wrappers
add_read_group [x] [x]
bamtools index [x] [x]
bamtools sort [x] [x]
bcl2fastq [x] [x]
blast makeblastdb [x]
busco [x]
bowtie1 align [x]
bowtie1 index [x]
bowtie2 index [x]
bowtie2 align [x]
bwa index [x]
bwa align [x]
bz2_to_gz [x]
canu [x]
deeptools/bam_coverage [x] [x]
dsrc_to_gz [x]
fastp [x]
fastqc [x] [x] [x]
fastq_stats [x]
falco [x] [x] [x]
feature_counts [x]
freebayes [x] [x]
freebayes_vcf_filter [x] [x]
gz_to_bz2 [x]
hmmer (build+scan) [x]
macs3 [x]
mark_duplicates [x]
medaka [x] [x]
multiqc [x]
minimap2 [x]
polypolish [x] [x]
rulegraph [x] [x] [x]
transdecoder longorf [x]
transcoder predicy [x]
salmon index [x] [x]
salmon mapping [x] [x]
samtools depth [x]
sambamba filter [x]
sambamba markdup [x]
sequana_coverage [x]
snpeff [x]
snpeff_add_locus_in_fasta [x] [x]
spades [x]
star [x] [x]
star [x] [x]
trinity [x]

Needed in pipelines

  • cutadapt.rules
  • spades_get_fastq.rules
  • spades.rules

not needed / deprecated / to be removed

  • joint_freebayes and joint_freebayes_filter_vcf are now redundant thanks to the wrappers
  • adapter_removal, alien_trimmer, identify_adapters: not used
  • chipuanar/chipuanar.rules: not used
  • conda/conda.rules: not used anymore
  • macs2

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

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