replikation
commented
4 years ago -
log
[skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [30/6a4185] process > discard_short (22) [100%] 29 of 29, cached: 29 ✔ [99/6d47b2] process > merge (1) [100%] 1 of 1, cached: 1 ✔ [49/bed4c9] process > fastp (1) [100%] 1 of 1, cached: 1 ✔ [6b/b6db04] process > sourmash_genome_size (1) [100%] 1 of 1, cached: 1 ✔ [9c/7e0b54] process > flye (1) [100%] 1 of 1, cached: 1 ✔ [b1/80004f] process > minimap_polish (1) [100%] 1 of 1, cached: 1 ✔ [b4/88391c] process > racon (1) [100%] 1 of 1, cached: 1 ✔ [0a/1b1f59] process > medaka (1) [100%] 1 of 1, cached: 1 ✔ [6e/457e6e] process > pilon (1) [100%] 1 of 1, cached: 1 ✔ [e9/f7cfcf] process > minimap2 (1) [100%] 1 of 1, cached: 1 ✔ [70/315a7d] process > bwa (1) [100%] 1 of 1, cached: 1 ✔ [e2/6c8269] process > metabat2 (1) [100%] 1 of 1, cached: 1 ✔ [18/f49bd2] process > maxbin2 (1) [100%] 1 of 1, cached: 1 ✔ [d5/46b334] process > concoct (1) [100%] 1 of 1, cached: 1 ✔ [2f/da86d3] process > refine3 (1) [100%] 1 of 1 ✔ [ff/67813b] process > checkm (1) [100%] 1 of 1 ✔ [f3/187f86] process > sourmash_bins (2) [100%] 2 of 2, failed: 2 [- ] process > sourmash_checkm_parser - [ef/5d2976] process > eggnog_download_db [100%] 1 of 1, cached: 1 ✔ [30/f09c21] process > eggnog_bin (3) [100%] 1 of 1 [- ] process > parser_bin - WARN: Process `eggnog_bin` publishDir path contains a variable with a null value -
also nextflow 20.01 is out so you dont need to write params behind modules anymore
whats missing
there is an incompatibility with sourmash and the lca database
i could not test the last parsers (use any simple ubuntu/python docker for these)
otherwise everything was working throughout the flye part