pcantalupo
/ gist:8600b2dddbb0c05784f827a4ccb48c8f
Created
July 23, 2020 12:07
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| $ nextflow run nf-core/rnaseq -c myconfig.config --aligner hisat2 --pseudo_aligner salmon -r dev --reads 'reads/*_tu_KAM56A3_S17.{1,2}.fq.gz' --reverseStranded --fasta GRCh38.d1.vd1.fa --gtf gencode.v22.annotation.gtf --skipBiotypeQC --removeRiboRNA | |
| N E X T F L O W ~ version 20.04.1 | |
| Launching `nf-core/rnaseq` [kickass_noyce] - revision: e14e0d4912 [dev] | |
| Extracting transcript fastas from genome fasta + gtf/gff | |
| RSEM only works with STAR. Disabling RSEM. | |
| WARN: The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { gtfFile }` | |
| ---------------------------------------------------- | |
| ,--./,-. | |
| ___ __ __ __ ___ /,-._.--~' | |
| |\ | |__ __ / ` / \ |__) |__ } { |
pcantalupo
/ gist:c5ae6644c42006453dadb6aee6f0b3be
Created
July 22, 2020 12:44
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| Error executing process > 'featureCounts (TPF-18-103_tu_KAM56A3_S17.1)' | |
| Caused by: | |
| Process `featureCounts (TPF-18-103_tu_KAM56A3_S17.1)` terminated with an error exit status (255) | |
| Command executed: | |
| featureCounts -a genes.gtf -g gene_id -t exon -o TPF-18-103_tu_KAM56A3_S17.1.sorted_gene.featureCounts.txt --extraAttributes gene_name -p -s 2 TPF-18-103_tu_KAM56A3_S17.1.sorted.bam | |
| featureCounts -a genes.gtf -g gene_biotype -o TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.featureCounts.txt -p -s 2 TPF-18-103_tu_KAM56A3_S17.1.sorted.bam | |
| cut -f 1,7 TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype.featureCounts.txt | tail -n +3 | cat biotypes_header.txt - >> TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_mqc.txt && mqc_features_stat.py TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_mqc.txt -s TPF-18-103_tu_KAM56A3_S17.1.sorted -f rRNA -o TPF-18-103_tu_KAM56A3_S17.1.sorted_biotype_counts_gs_mqc.tsv |
pcantalupo
/ gist:777245d01f2ece930f96618e28037053
Created
July 14, 2020 13:02
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| #gtf-version 2.2 | |
| #!genome-build ViralProj14074 | |
| #!genome-build-accession NCBI_Assembly:GCF_000837865.1 | |
| NC_001538.1 RefSeq gene 388 588 . + . gene_id "BKPyVgp1"; db_xref "GeneID:29031013"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "BKPyVgp1"; | |
| NC_001538.1 RefSeq CDS 388 585 . + 0 gene_id "BKPyVgp1"; transcript_id "unknown_transcript_1"; db_xref "GOA:P03085"; db_xref "InterPro:IPR002643"; db_xref "UniProtKB/Swiss-Prot:P03085"; gbkey "CDS"; locus_tag "BKPyVgp1"; product "agnoprotein"; protein_id "YP_717936.1"; | |
| NC_001538.1 RefSeq start_codon 388 390 . + 0 gene_id "BKPyVgp1"; transcript_id "unknown_transcript_1"; db_xref "GOA:P03085"; db_xref "InterPro:IPR002643"; db_xref "UniProtKB/Swiss-Prot:P03085"; gbkey "CDS"; locus_tag "BKPyVgp1"; product "agnoprotein"; protein_id "YP_717936.1"; | |
| NC_001538.1 RefSeq stop_codon 586 588 . + 0 gene_id "BKPyVgp1"; transcript_id "unknown_transcript_1"; db_xref "GOA:P03085"; db_xref "InterPro:IPR002643"; db_xref "UniProtKB/Swiss-Prot:P03085"; gbkey "CDS"; locus_tag "BK |
pcantalupo
/ ChordNetwork
Created
June 30, 2020 12:14
— forked from fusaroli/ChordNetwork
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| # Assuming you have a matrix (CorMat_S) with a structure like a correlation matrix | |
| # Load the libraries (NB probably some superfluous ones, I haven't double-checked) | |
| pacman::p_load( | |
| # General utility functions | |
| tidyverse, | |
| # Plotting | |
| ggplot2, | |
| scales, | |
| ggstance, |
pcantalupo
/ nfcorernaseq05102020
Created
May 11, 2020 14:58
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| 130 dnanexus@job-Fpqyjj0014vg89F98195yqxP:~/RNA-Seq⟫ sudo ~/nextflow run nf-core/rnaseq -profile docker --aligner hisat2 -r 1.4.2 --pseudo_aligner salmon --reads 'data/*_{1,2}.fastq' --reverseStranded --fasta Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa.gz --gtf Homo_sapiens.GRCh38.90_withBKV.gtf.gz --max_memory 30GB | |
| N E X T F L O W ~ version 20.04.1 | |
| Launching `nf-core/rnaseq` [sick_hamilton] - revision: 3b6df9bd10 [1.4.2] | |
| Extracting transcript fastas from genome fasta + gtf/gff | |
| ---------------------------------------------------- | |
| ,--./,-. | |
| ___ __ __ __ ___ /,-._.--~' | |
| |\ | |__ __ / ` / \ |__) |__ } { | |
| | \| | \__, \__/ | \ |___ \`-._,-`-, | |
| `._,._,' |
pcantalupo
/ mock_dependency.nf
Created
May 3, 2020 01:48
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| #!/usr/bin/env nextflow | |
| //https://nextflow-io.github.io/patterns/index.html#_mock_dependency | |
| echo true | |
| process s1 { | |
| output: | |
| val true into done_ch | |
| script: |
pcantalupo
/ foo8190.fa
Created
May 1, 2020 17:04
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| >foo | |
| AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
pcantalupo
/ nextflow_fileurl
Created
April 21, 2020 15:18
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| dockerfile = 'https://raw.githubusercontent.com/pcantalupo/ViraVate/master/Dockerfile' | |
| println dockerfile // print variable | |
| file_dockerfile = file(dockerfile) | |
| println file_dockerfile.text // print contents of file (pulled from remote location) | |
| df_ch = Channel.fromPath(dockerfile) | |
| process foo { | |
| echo true |
pcantalupo
/ nextflow_BKV_samtools_bam_mem_error
Created
April 16, 2020 19:40
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| $ nextflow run nf-core/rnaseq -profile docker --aligner hisat2 -r 1.4.2 --reads 'data/*_{1,2}_10k.fastq' --reverseStranded --max_cpus 6 --max_memory 32 -c config_bkv.txt | |
| NOTE: Nextflow is not tested with Java 13.0.2 -- It's recommended the use of version 8 up to 12 | |
| N E X T F L O W ~ version 20.01.0 | |
| Launching `nf-core/rnaseq` [nostalgic_solvay] - revision: 3b6df9bd10 [1.4.2] | |
| ---------------------------------------------------- | |
| ,--./,-. | |
| ___ __ __ __ ___ /,-._.--~' | |
| |\ | |__ __ / ` / \ |__) |__ } { | |
| | \| | \__, \__/ | \ |___ \`-._,-`-, |
pcantalupo
/ nextflow_BKV_salmon_quant_error
Created
April 16, 2020 19:35
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| $ nextflow run nf-core/rnaseq -profile docker --aligner hisat2 -r 1.4.2 --pseudo_aligner salmon --reads 'data/*_{1,2}_10k.fastq' --reverseStranded --max_cpus 6 --max_memory 32 -c config_bkv.txt | |
| NOTE: Nextflow is not tested with Java 13.0.2 -- It's recommended the use of version 8 up to 12 | |
| N E X T F L O W ~ version 20.01.0 | |
| Launching `nf-core/rnaseq` [cheesy_northcutt] - revision: 3b6df9bd10 [1.4.2] | |
| Extracting transcript fastas from genome fasta + gtf/gff | |
| ---------------------------------------------------- | |
| ,--./,-. | |
| ___ __ __ __ ___ /,-._.--~' | |
| |\ | |__ __ / ` / \ |__) |__ } { |