concept: metagen_painter

[colindaven]

• [ ] easy concept
• [x] 1. take some output file eg reporting
• [x] Don't use haybaler output file (wait - this is a matrix, so v tricky)
• [x] 2. take directory of input files - eg raspir
• [x] 3. "paint" an extra column of whether the species was raspir_positive or raspir_negative in that sample
• [ ] 4. other options - krakenuniq, growth_rate (with rate) etc
• [ ] 5. need to consider parameters

implies wochenende -> reporting -> metagen_painter -> haybaler (eg on specified samples, eg raspir_positive

[colindaven]

Wow, thanks Lisa @LisaHollstein , this works already. I have a lot of tidying to do in the nextflow script, but it works already and is a great start based on this new nextflow technology. Great work.

Going forwards, we need to consider how we deal with the files. Maybe std out within nextflow is the best option, for instance when we want to add kraken or metaphlan columns in too.

Initial data integration looks really nice though!

[colindaven]

This is what I get on the test data, which looks great

grep pir_pos 1_sm_R1.ndp.trm.s.mm.dup.mq30.bam.txt.rep.us.csv.nf_reporting.csv  | cut -f2 -d,
1_AE005672_3_Streptococcus_pneumoniae_TIGR4__complete_genome_BAC
1_AE009951_2_Fusobacterium_nucleatum_subsp__nucleatum_ATCC_25586__complete_genome_BAC
1_AP011540_1_Rothia_mucilaginosa_DY_18_DNA__complete_genome_BAC
1_CP000792_2_Campylobacter_concisus_13826__complete_genome_BAC
1_CP001685_1_Leptotrichia_buccalis_DSM_1135__complete_genome_BAC
1_CP001721_1_Atopobium_parvulum_DSM_20469__complete_genome_BAC
1_CP001820_1_Veillonella_parvula_DSM_2008__complete_genome_BAC
1_CP002122_1_Prevotella_melaninogenica_ATCC_25845_chromosome_I__complete_sequence_BAC
1_CP002589_1_Prevotella_denticola_F0289__complete_genome_BAC
1_CP002843_1_Streptococcus_parasanguinis_ATCC_15912__complete_genome_BAC
1_CP002925_1_Streptococcus_pseudopneumoniae_IS7493__complete_genome_BAC
1_CP007726_1_Neisseria_elongata_subsp__glycolytica_ATCC_29315__complete_genome_BAC
1_CP012072_1_Actinomyces_meyeri_strain_W712__complete_genome_BAC
1_CP012074_1_Prevotella_fusca_JCM_17724_strain_W1435_chromosome_1__complete_sequence_BAC
1_CP013195_1_Prevotella_enoeca_strain_F0113__complete_genome_BAC
1_CP013336_1_Fusobacterium_hwasookii_ChDC_F206__complete_genome_BAC
1_CP020438_2_Streptococcus_equinus_strain_FDAARGOS_251_chromosome__complete_genome_BAC
1_CP020452_2_Neisseria_mucosa_strain_FDAARGOS_260_chromosome__complete_genome_BAC
1_CP020566_1_Veillonella_atypica_strain_OK5_chromosome__complete_genome_BAC
1_CP023863_1_Prevotella_jejuni_strain_CD3_33_chromosome_I__complete_sequence_BAC
1_CP024698_1_Fusobacterium_periodonticum_strain_KCOM_1283_chromosome__complete_genome_BAC
1_FN568063_1_Streptococcus_mitis_B6_complete_genome__strain_B6_BAC
1_FQ312002_1_Haemophilus_parainfluenzae_T3T1_complete_genome_BAC
1_FR720602_1_Streptococcus_oralis_Uo5_complete_genome_sequence_BAC
1_FR873482_1_Streptococcus_salivarius_JIM8777_complete_genome_BAC
NZ_LR134484.1_Gemella_haemolysans_strain_NCTC10459_chromosome_1
NZ_CP040006.1_Schaalia_odontolytica_strain_XH001_chromosome__complete_genome
NZ_LR134375.1_Veillonella_dispar_strain_NCTC11831_chromosome_1
NZ_CP031251.1_Neisseria_subflava_strain_M18660_chromosome__complete_genome
NZ_LS483369.1_Neisseria_cinerea_strain_NCTC10294_chromosome_1