taxprofiler/modules.json

{
    "name": "nf-core/taxprofiler",
    "homePage": "https://github.com/nf-core/taxprofiler",
    "repos": {
        "nf-core/modules": {
            "adapterremoval": {
                "git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
            },
            "bbmap/bbduk": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "bowtie2/align": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "bowtie2/build": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "cat/fastq": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "centrifuge/centrifuge": {
                "git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
            },
            "centrifuge/kreport": {
                "git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
            },
            "custom/dumpsoftwareversions": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "diamond/blastx": {
                "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
            },
            "fastp": {
                "git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
            },
            "fastqc": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "filtlong": {
                "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
            },
            "gunzip": {
                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
            },
            "kaiju/kaiju": {
                "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
            },
            "kaiju/kaiju2krona": {
                "git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
            },
            "kaiju/kaiju2table": {
                "git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
            },
            "kraken2/kraken2": {
                "git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
            },
            "krakentools/kreport2krona": {
                "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
            },
            "krona/ktimporttaxonomy": {
                "git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
            },
            "krona/ktimporttext": {
                "git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
            },
            "malt/run": {
                "git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
            },
            "megan/rma2info": {
                "git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
            },
            "metaphlan3": {
                "git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
            },
            "minimap2/align": {
                "git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
            },
            "minimap2/index": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "motus/merge": {
                "git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
            },
            "motus/profile": {
                "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
            },
            "multiqc": {
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
            },
            "porechop": {
                "git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
            },
            "prinseqplusplus": {
                "git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
            },
            "samtools/bam2fq": {
                "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
            },
            "samtools/view": {
                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
            },
            "untar": {
                "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
            }
        }
    }
}
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`{`
			`"name": "nf-core/taxprofiler",`
			`"homePage": "https://github.com/nf-core/taxprofiler",`
			`"repos": {`
			`"nf-core/modules": {`
Start working on adding adapterremoval 2022-03-31 13:31:45 +00:00			`"adapterremoval": {`
chore: update adapterremoval 2022-04-05 08:18:34 +00:00			`"git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"`
Start working on adding adapterremoval 2022-03-31 13:31:45 +00:00			`},`
Add bbduk complexity (entropy-based) filtering 2022-04-02 15:02:05 +00:00			`"bbmap/bbduk": {`
			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
Start working on adding adapterremoval 2022-03-31 13:31:45 +00:00			`},`
Start work on host removal 2022-04-03 05:58:40 +00:00			`"bowtie2/align": {`
			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
			`},`
			`"bowtie2/build": {`
			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
			`},`
Get skeleton read processing to input for profiling 2022-02-18 15:51:01 +00:00			`"cat/fastq": {`
			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
			`},`
Check if PR works with centrifuge/centrifuge module 2022-04-07 14:13:17 +00:00			`"centrifuge/centrifuge": {`
			`"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"`
			`},`
Add centrifuge kreport in taxprofiler 2022-04-22 13:24:10 +00:00			`"centrifuge/kreport": {`
Update centrifuge/kreport 2022-07-27 12:44:26 +00:00			`"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"`
Add centrifuge kreport in taxprofiler 2022-04-22 13:24:10 +00:00			`},`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`"custom/dumpsoftwareversions": {`
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`},`
Add draft version of DIAMOND 2022-04-29 19:59:42 +00:00			`"diamond/blastx": {`
Update the dev branch with the DIAMOND module update 2022-07-15 14:28:07 +00:00			`"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"`
Add draft version of DIAMOND 2022-04-29 19:59:42 +00:00			`},`
Get skeleton read processing to input for profiling 2022-02-18 15:51:01 +00:00			`"fastp": {`
			`"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"`
			`},`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`"fastqc": {`
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`},`
Add initial longread QC filtering - requires filtlong module update 2022-05-01 05:18:14 +00:00			`"filtlong": {`
Update filtlong module 2022-07-12 15:43:52 +00:00			`"git_sha": "957cb9b83668075f4af101fc99502908cca487e3"`
Add initial longread QC filtering - requires filtlong module update 2022-05-01 05:18:14 +00:00			`},`
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file 2022-06-30 16:33:11 +00:00			`"gunzip": {`
			`"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"`
			`},`
Add centrifuge kreport in taxprofiler 2022-04-22 13:24:10 +00:00			`"kaiju/kaiju": {`
			`"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"`
			`},`
Install KAIJU_KAIJU2KRONA 2022-06-27 13:58:28 +00:00			`"kaiju/kaiju2krona": {`
			`"git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"`
			`},`
Add kaiju2table to taxprofiler 2022-04-25 15:36:29 +00:00			`"kaiju/kaiju2table": {`
			`"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"`
			`},`
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 16:42:02 +00:00			`"kraken2/kraken2": {`
Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 03:22:35 +00:00			`"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"`
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 16:42:02 +00:00			`},`
Install KRAKENTOOLS_KREPORT2KRONA module 2022-06-14 13:13:36 +00:00			`"krakentools/kreport2krona": {`
			`"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"`
			`},`
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file 2022-06-30 16:33:11 +00:00			`"krona/ktimporttaxonomy": {`
Get fixed Krona module and add Krona taxonomy to test profile 2022-07-01 15:21:19 +00:00			`"git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"`
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file 2022-06-30 16:33:11 +00:00			`},`
Install KRONA_KTIMPORTTEXT 2022-06-14 13:27:42 +00:00			`"krona/ktimporttext": {`
			`"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"`
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 16:42:02 +00:00			`},`
			`"malt/run": {`
Roll back MALT version 2022-06-20 06:23:14 +00:00			`"git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"`
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 16:42:02 +00:00			`},`
Start work 2022-04-13 09:49:35 +00:00			`"megan/rma2info": {`
			`"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"`
			`},`
chore: add metaphlan3 module 2022-03-18 14:38:19 +00:00			`"metaphlan3": {`
Add modules 2022-05-03 07:28:46 +00:00			`"git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"`
			`},`
			`"minimap2/align": {`
			`"git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"`
			`},`
			`"minimap2/index": {`
chore: add metaphlan3 module 2022-03-18 14:38:19 +00:00			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
			`},`
Add motus/merge and biom support 2022-07-12 09:39:26 +00:00			`"motus/merge": {`
			`"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"`
			`},`
add motus profile. 2022-05-23 12:05:06 +00:00			`"motus/profile": {`
Fix modules JSON 2022-07-15 10:38:20 +00:00			`"git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"`
add motus profile. 2022-05-23 12:05:06 +00:00			`},`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`"multiqc": {`
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"`
Start getting database prep ready 2022-03-21 14:07:59 +00:00			`},`
Add Porechop module 2022-03-18 13:34:10 +00:00			`"porechop": {`
Add emitting porechop logs to multiqc and fix collection of others 2022-07-19 11:50:39 +00:00			`"git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"`
Fix kraken2 module 2022-03-28 14:46:45 +00:00			`},`
Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`"prinseqplusplus": {`
			`"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"`
			`},`
Add modules 2022-05-03 07:28:46 +00:00			`"samtools/bam2fq": {`
Update samtools/bam2fq 2022-05-05 06:38:41 +00:00			`"git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"`
Add modules 2022-05-03 07:28:46 +00:00			`},`
			`"samtools/view": {`
Update samtools view 2022-05-03 09:09:54 +00:00			`"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"`
Add modules 2022-05-03 07:28:46 +00:00			`},`
Fix kraken2 module 2022-03-28 14:46:45 +00:00			`"untar": {`
			`"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`}`
			`}`
			`}`
fix the end line issue for modules.json 2022-05-25 12:03:23 +00:00			`}`