diff --git a/CHANGELOG.md b/CHANGELOG.md
index b938f472..da540360 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## nf-core/ampliseq version 2.11.0dev
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+- [#760](https://github.com/nf-core/ampliseq/pull/760) - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0
+
+### `Dependencies`
+
+### `Removed`
+
 ## nf-core/ampliseq version 2.10.0 - 2024-06-27
 
 ### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 0a63581f..ec828d82 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.10.0" target="_blank">nf-core/ampliseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/tree/dev" target="_blank">nf-core/ampliseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/ampliseq/2.10.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/ampliseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-ampliseq-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 81124505..7e0a4025 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -356,7 +356,7 @@ manifest {
     description     = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.10.0'
+    version         = '2.11.0dev'
     doi             = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
 }
 
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index fa221126..5105b545 100644
--- a/workflows/ampliseq.nf
+++ b/workflows/ampliseq.nf
@@ -268,13 +268,13 @@ workflow AMPLISEQ {
     ch_input_reads = Channel.empty()
     if ( params.input ) {
         // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
-        ch_input_reads = Channel.fromSamplesheet("input")
+        ch_input_reads = Channel.fromSamplesheet("input") // meta: meta.sample, meta.run
             .map{ meta, readfw, readrv ->
                 meta.single_end = single_end.toBoolean()
                 def reads = single_end ? readfw : [readfw,readrv]
-                if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.id, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isnt specified
-                if ( !meta.single_end && ( readfw.getSimpleName() == meta.id || readrv.getSimpleName() == meta.id ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.id") } // sample name and any file name without extensions arent identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
-                if ( meta.single_end && ( readfw.getSimpleName() == meta.id+"_1" || readfw.getSimpleName() == meta.id+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.id") } // sample name and file name without extensions arent identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
+                if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.sample, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isnt specified
+                if ( !meta.single_end && ( readfw.getSimpleName() == meta.sample || readrv.getSimpleName() == meta.sample ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and any file name without extensions arent identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
+                if ( meta.single_end && ( readfw.getSimpleName() == meta.sample+"_1" || readfw.getSimpleName() == meta.sample+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and file name without extensions arent identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
                 return [meta, reads] }
     } else if ( params.input_fasta ) {
         ch_input_fasta = Channel.fromPath(params.input_fasta, checkIfExists: true)