Install RCLONE_* modules

CHANGELOG.md

@@ -13,6 +13,7 @@ Initial release of nf-core/datasync, created with the [nf-core](https://nf-co.re
 - [[#35](https://github.com/nf-core/datasync/pull/35)] - Compare generated checksum to given checksum in input and update test profiles ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
 - [[#46](https://github.com/nf-core/datasync/pull/46)] - Import Rclone module from nf-core([@antoniasaracco](https://github.com/antoniasaracco), review by [@delfiterradas](https://github.com/delfiterradas)).
 - [[#41](https://github.com/nf-core/datasync/pull/41)] - Generate MultiQC Report with comparechecksum tables and input samplesheet ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
+- [[#49](https://github.com/nf-core/datasync/pull/49)] - Install `RCLONE_CHECK` and `RCLONE_CHECKSUM` modules from nf-core ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@antoniasaracco](https://github.com/antoniasaracco)).
 
 ### `Fixed`
 

assets/multiqc_config.yml

@@ -31,87 +31,36 @@ custom_data:
       checksum_sha:
         title: Sha256 checksum file
 
-  md5_checksum_summary:
-    section_name: "MD5 Checksum Summary"
-    description: "Summary of MD5 checksum validation"
+  rclone_checksum_md5:
+    section_name: "MD5sum Input Validation"
+    description: "Comparison of the expected MD5 checksums provided in the samplesheet with the observed MD5 checksums of the file(s) found at the specified source path."
     plot_type: "table"
-    file_format: "csv"
-    headers:
-      Match:
-        description: "Number of files whose output checksum matches the expected checksum."
-      Mismatch:
-        description: "Number of files whose output checksum differs from the expected checksum."
-      Missing:
-        description: "Number of expected input files that are missing from the output."
-      Unexpected:
-        description: "Number of output files that were not present in the input checksum list."
-
-  sha_checksum_summary:
-    section_name: "SHA Checksum Summary"
-    description: "Summary of SHA checksum validation"
-    plot_type: "table"
-    file_format: "csv"
-    headers:
-      Match:
-        description: "Number of files whose output checksum matches the expected checksum."
-      Mismatch:
-        description: "Number of files whose output checksum differs from the expected checksum."
-      Missing:
-        description: "Number of expected input files that are missing from the output."
-      Unexpected:
-        description: "Number of output files that were not present in the input checksum list."
+    file_format: "tsv"
+    pconfig:
+      no_violin: true
 
-  md5_checksum_report:
-    section_name: "MD5 Checksum Report"
-    description: "Detailed MD5 checksum validation report"
+  rclone_checksum_sha:
+    section_name: "SHAsum Input Validation"
+    description: "Comparison of the expected SHA-256 checksums provided in the samplesheet with the observed SHA-256 checksums of the file(s) found at the specified source path."
     plot_type: "table"
-    file_format: "csv"
+    file_format: "tsv"
     pconfig:
       no_violin: true
-    headers:
-      File:
-        title: File
-        description: "Path to the file being validated."
-      checksum_expected:
-        title: Expected checksum
-        description: "Checksum recorded for the input file before processing."
-      checksum_observed:
-        title: Observed checksum
-        description: "Checksum calculated for the corresponding output file after processing."
-      status:
-        title: Status
-        description: "Comparison result between the expected and observed checksums."
 
-  sha_checksum_report:
-    section_name: "SHA Checksum Report"
-    description: "Detailed SHA checksum validation report"
+  rclone_check:
+    section_name: "Source-Destination Checksum Validation"
+    description: "Comparison of the checksums of corresponding file(s) in the source input path and the output destination to confirm data integrity following file transfer."
     plot_type: "table"
-    file_format: "csv"
+    file_format: "tsv"
     pconfig:
       no_violin: true
-    headers:
-      File:
-        title: File
-        description: "Path to the file being validated."
-      checksum_expected:
-        title: Expected checksum
-        description: "Checksum recorded for the input file before processing."
-      checksum_observed:
-        title: Observed checksum
-        description: "Checksum calculated for the corresponding output file after processing."
-      status:
-        title: Status
-        description: "Comparison result between the expected and observed checksums."
 
 sp:
   samplesheet:
     fn: "samplesheet.csv"
-
-  md5_checksum_summary:
-    fn: "*_md5.checksum_summary.csv"
-  sha_checksum_summary:
-    fn: "*_sha.checksum_summary.csv"
-  md5_checksum_report:
-    fn: "*_md5.checksum_validation.csv"
-  sha_checksum_report:
-    fn: "*_sha.checksum_validation.csv"
+  rclone_checksum_md5:
+    fn: "*_md5_rclone_checksum_mqc.tsv"
+  rclone_checksum_sha:
+    fn: "*_sha_rclone_checksum_mqc.tsv"
+  rclone_check:
+    fn: "*_rclone_check_mqc.tsv"

conf/containers_conda_lock_files_amd64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }
+process { withName: 'RCLONE_CHECK' { container = 'modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'modules/nf-core/rclone/checksum/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt' } }
 process { withName: 'RCLONE_COPY' { container = 'modules/nf-core/rclone/copy/.conda-lock/linux_amd64-bd-ff88b2e0040147be_1.txt' } }

conf/containers_conda_lock_files_arm64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }
+process { withName: 'RCLONE_CHECK' { container = 'modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'modules/nf-core/rclone/checksum/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt' } }
 process { withName: 'RCLONE_COPY' { container = 'modules/nf-core/rclone/copy/.conda-lock/linux_arm64-bd-ff88b2e0040147be_1.txt' } }

conf/containers_docker_amd64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }
+process { withName: 'RCLONE_CHECK' { container = 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' } }
 process { withName: 'RCLONE_COPY' { container = 'community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } }

conf/containers_docker_arm64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }
+process { withName: 'RCLONE_CHECK' { container = 'community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a' } }
 process { withName: 'RCLONE_COPY' { container = 'community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } }

conf/containers_singularity_https_amd64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }
+process { withName: 'RCLONE_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' } }
 process { withName: 'RCLONE_COPY' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data' } }

conf/containers_singularity_https_arm64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }
+process { withName: 'RCLONE_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data' } }
 process { withName: 'RCLONE_COPY' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data' } }

conf/containers_singularity_oras_amd64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }
+process { withName: 'RCLONE_CHECK' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82' } }
 process { withName: 'RCLONE_COPY' { container = 'oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } }

conf/containers_singularity_oras_arm64.config

@@ -1,2 +1,4 @@
 process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }
+process { withName: 'RCLONE_CHECK' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d' } }
+process { withName: 'RCLONE_CHECKSUM' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d' } }
 process { withName: 'RCLONE_COPY' { container = 'oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } }

conf/modules.config

@@ -18,10 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: 'COMPARECHECKSUM' {
-        ext.prefix = { "${meta.id}_${meta.check_format}" }
-    }
-
     withName: 'RCLONE_COPY' {
         ext.args = {
             def base_args = [
@@ -39,6 +35,16 @@ process {
         }
     }
 
+    withName: 'RCLONE_CHECK' {
+        ext.args = {
+            def base_args = [
+                '--no-check-certificate',
+                '--one-way'
+            ]
+            base_args.join(' ')
+        }
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

modules.json

@@ -5,24 +5,24 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "md5sum": {
+                    "multiqc": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                         "installed_by": ["modules"]
                     },
-                    "multiqc": {
+                    "rclone/check": {
                         "branch": "master",
-                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
+                        "git_sha": "0983b1ef5f0729946953d921100af925f86fafb0",
                         "installed_by": ["modules"]
                     },
-                    "rclone/copy": {
+                    "rclone/checksum": {
                         "branch": "master",
-                        "git_sha": "969013a2a91dc8152ca537bbd4dd4feaa15c13a7",
+                        "git_sha": "0983b1ef5f0729946953d921100af925f86fafb0",
                         "installed_by": ["modules"]
                     },
-                    "shasum": {
+                    "rclone/copy": {
                         "branch": "master",
-                        "git_sha": "429d56ab5b5879549f71bf9905104f39d0c3bff4",
+                        "git_sha": "969013a2a91dc8152ca537bbd4dd4feaa15c13a7",
                         "installed_by": ["modules"]
                     }
                 }