# TOFU-MAaPO https://github.com/ikmb/TOFU-MAaPO mmu_genome:https://benlangmead.github.io/aws-indexes/bowtie ## /home/changrong/Desktop/jg6_metagenomics_TOFU 30site ./nextflow-23.04.1-all run ~/TOFU-MAaPO-1.3.2/ --reads sample.csv -profile custom --humann -resume --genome human --kraken --metaphlan ## 31 site /data3/zhiyu/software/TOFU/test /home/zhiyu/data/script/TOFU_16S/nextflow-23.04.1-all run /data3/zhiyu/software/TOFU/TOFU-MAaPO-1.40/ --reads fq_test.csv -profile custom --magscot --assembly -resume --outdir result ./nextflow-23.04.1-all run ikmb/TOFU-MAaPO -r 1.4.0 --reads '/data3/zhiyu/rawdata/16S/221028_C70164_0089_000000000-K7RN4/*_R{1,2}_001.fastq.gz' -profile /data3/zhiyu/software/TOFU/TOFU-MAaPO-1.40/conf/custom.config --humann -resume --genome human --kraken --metaphlan // 小鼠 nextflow run ikmb/TOFU-MAaPO -r 1.4.0 --reads 'ceshi/rawdata/*_R{1,2}_001.fastq.gz' -profile custom --humann -resume --genome human --kraken --metaphlan --kraken2_db '/data3/zhiyu/Database/TOFU/MGBC-26640_KrakenBracken' // 人的 nextflow run ikmb/TOFU-MAaPO -r 1.4.0 --reads 'ceshi/rawdata/*_R{1,2}_001.fastq.gz' -profile custom --humann -resume --genome human --kraken --metaphlan --kraken2_db '/data3/zhiyu/Database/TOFU/UHGG_v2.0.2' // 默认的 nextflow run ikmb/TOFU-MAaPO -r 1.4.0 --reads '/data3/zhiyu/pipelines/shotgun/test/ceshi/rawdata/*_R{1,2}_001.fastq.gz' -profile custom --humann --genome human --kraken --metaphlan #need copy custom.config /home/zhiyu/data/script/TOFU_16S/nextflow-23.04.1-all run ikmb/TOFU-MAaPO -r 1.4.0 --reads fq_test.csv -profile custom --magscot --assembly -resume --outdir result # Note fq必须是以gz结尾 gzip *fq https://github.com/biobakery/biobakery/wiki/humann3#23-humann-default-outputs https://github.com/biobakery/humann/blob/master/humann/tools/regroup_table.py#L44 runOptions = "-B /data3/zhiyu" #目录层级不能太多 3.213.10.33 quay.io 172.64.150.58 cdn03.quay.io /etc/init.d/networking restart # 自动删掉work directory 可以直接在nextflow.config文件里加上cleanup=true https://www.nextflow.io/docs/latest/config.html#miscellaneous 跑完就自动删掉了work directory